Bonham Carter started a relationship with actor/director Kenneth Branagh (while he was married to actress Emma Thompson) during the filming of Frankenstein, which lasted until the summer of 1999; she appeared in several films afterward with Branagh, a pattern she repeated in subsequent relationships. She then briefly dated actors Rufus Sewell and Steve Martin. In October 2001, she began her current relationship with director Tim Burton (while he was engaged to and living with actress Lisa Marie, who was also Burton collaborator and co-producer), whom she met while filming Planet of the Apes. Burton has taken to casting Bonham Carter in his movies, including Big Fish, The Corpse Bride, Charlie and the Chocolate Factory, and Sweeney Todd. They live in Belsize Park, London, in adjoining houses with a connecting hallway, each part decorated and styled to suit their own personalities, because they felt they couldn't live 'together' but didn't want to live apart.

They purchased the house when she became pregnant with the couple's first child, son Billy Ray Burton, who was born on 4 October 2003. The couple maintain a close relationship with actor Johnny Depp, who regularly appears in most of Burton's films, he is also Billy Ray's godfather, accepting the job after Burton persuaded Bonham Carter to ask him. At age 41, she gave birth to her second child, a daughter named Nell Burton, on 15 December 2007 in Central London. She says she named her daughter Nell after all the "Helens" in her family lineage. In August 2008, four of her relatives were killed in a safari bus crash in South Africa, she was given indefinite leave from filming Terminator Salvation, and returned later on to complete the rest of her filming.

In 2008, both Bonham Carter and Burton put their American apartments up for sale. The apartments are located in the Greenwich Village area, in New York City. The couple sold them for a collective $8.75 million. In early October 2008, it was released that Bonham Carter had become a patron of the charity, Action Duchenne, the national charity established to support parents and sufferers of Duchenne Muscular Dystrophy. Bonham Carter released the statement:

"As a patron of Action Duchenne, I would like to urge as many people as possible to find out about the work of the charity and the devastating effects of Duchenne Muscular Dystrophy. Treatments and a cure seem tantalisingly close but they will not appear without further support and funding. Please join Action Duchenne in helping to make muscle wasting history."

In December 2008, Bonham Carter lent her voice to a MTV domestic violence public service announcement, reciting a passage about love from the book of Corinthians in the Bible. The 60-second commercial, created by ad agency Ogilvy Advertising, features a dysfunctional couple in a domestic environment. No dialogue is heard — only accompanying music and Bonham Carter's voice reciting Love is Patient, Love is Kind from 1 Corinthians, Chapter 13, verse four. Bonham Carter recorded her vocal in a single take for the ad, which broke on December 2, 2008. The ad will air across MTV in the UK and across Europe as part of MTV's Staying Alive campaign. MTV will also make the ad available online and is considering running it in cinemas.

• Harry Potter and the Deathly Hallows: Part II (2011) (pre-production) .... Bellatrix Lestrange
• Harry Potter and the Deathly Hallows: Part I (2010) (pre-production) .... Bellatrix Lestrange
  ... aka The Deathly Hallows (USA: short title)
• Lorelei (2009) (pre-production) (rumored) .... Gillian Livingston
• Alice in Wonderland (2010) (filming) .... The Red Queen
• Terminator Salvation (2009) (post-production) .... Serena
  ... aka Terminator: Die Erlösung (Germany)
• Harry Potter and the Half-Blood Prince (2009) (completed) .... Bellatrix Lestrange
  ... aka HP and the HBP (International: English title: informal short title)
  ... aka Harry Potter and the Half-Blood Prince: An IMAX 3D Experience (USA: IMAX version)
  ... aka The Half-Blood Prince (USA: short title)
  
• Sweeney Todd: The Demon Barber of Fleet Street (2007) .... Mrs. Lovett
  ... aka Sweeney Todd (USA: short title)
• Harry Potter and the Order of the Phoenix (2007) .... Bellatrix Lestrange
  ... aka Harry Potter and the Order of the Phoenix: The IMAX Experience (USA: IMAX version)
  ... aka The Order of the Phoenix (USA: short title)
• Sixty Six (2006) .... Esther Reubens
• Magnificent 7 (2005) (TV) .... Maggi
• Wallace & Gromit: The Curse of the Were-Rabbit (2005/I) (VG) (voice) .... Lady Tottington
• Corpse Bride (2005) (voice) .... Corpse Bride
  ... aka Tim Burton's Corpse Bride (Singapore: English title) (USA: complete title)
• Wallace & Gromit in The Curse of the Were-Rabbit (2005) (voice) .... Lady Campanula Tottington
  ... aka Wallace & Gromit: The Curse of the Were-Rabbit (UK: poster title)
• Conversations with Other Women (2005) .... Woman
• Charlie and the Chocolate Factory (2005) .... Mrs. Bucket
  ... aka Charlie and the Chocolate Factory: The IMAX Experience (USA: IMAX version)
• Big Fish (2003) .... Jenny - Young / Jenny - Senior / The Witch
• Henry VIII (2003) (TV) .... Anne Boleyn
• Live from Baghdad (2002) (TV) .... Ingrid Formanek
• Till Human Voices Wake Us (2002) .... Ruby
• The Heart of Me (2002) .... Dinah
• Novocaine (2001) .... Susan
• Planet of the Apes (2001) .... Ari
• Football (2001) (as Helena Bonham-Carter) .... Mum
• Carnivale (2000) (voice) .... Milly
  ... aka Carnivale (France)
  
• The Nearly Complete and Utter History of Everything (1999) (TV) .... Lily
• Women Talking Dirty (1999) .... Cora
• Fight Club (1999) .... Marla Singer