In 1998, O'Donnell and former Nickelodeon executive Kelli Carpenter became partners. On November 29, 2002, Carpenter gave birth to the couple's fourth child, Vivienne Rose O'Donnell. O'Donnell and Carpenter were married in San Francisco on February 26, 2004, during the brief period that Mayor Gavin Newsom permitted same-sex marriages in the city. Their marriage was subsequently nullified by the California Supreme Court.

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In addition to raising her children and hosting her television show, O'Donnell has established her own charity organization, called For All Kids Foundation, and launched her own magazine, Rosie.

In a flurry of charges and countercharges, O'Donnell ended her association with the magazine in mid-2002. The departure led to a suit and countersuit between O'Donnell and publisher Gunner + Jahr. The bitter legal dispute ended in November 2003, with a judge's ruling that neither party deserved damages.

In 2003, O'Donnell produced Taboo, a musical about the life of Leigh Bowery, with music by Boy George. The show opened to tepid reviews, but ran for some 100 performances on Broadway.

In 2006, O'Donnell accepted an invitation to serve as moderator of the television talk show The View. Her presence immediately boosted ratings, but she became a lightening rod for controversy, especially because of her strong opinions about the Bush administration's policies in Iraq. She left the show after a few months.

In 2007, she released a second memoir, Celebrity Detox, in which she discusses her time at The View and her struggle with fame.

In 2008, O'Donnell produced and starred in a Lifetime Television movie entitled America, in which she played a therapist to a teenager in the foster care system.

In 2009, she inaugurated Rosie Radio, a two-hour daily program on Sirius XM Radio.

Also in 2009, O'Donnell announced that she and Carpenter had separated. She was subsequently linked with artist Tracy Kachtik-Anders, but the couple never lived together and the relationship ended in 2011.

In 2011, O'Donnell signed on with OWN: Oprah Winfrey Network to return to daytime TV with another talk show, The Rosie Show. On March 16, 2012, the OWN Network cancelled the show due to low ratings. The final episode aired on March 29, 2012.