According to Flynt's autobiography, his first sexual experience was a mistaken encounter with a chicken after he'd heard from older boys that sex with chicken was similar in sensation to sexual intercourse with a woman. He proceeded to have sex with a chicken killing it afterwards to avoid any suspicion.

He was married five times, the longest marriage was to his fourth wife, Althea, from 1976 until her death in 1987. She had been suffering from AIDS and drowned in a bath tub, possibly as a result of a heroin overdose. He has five children.

He had a one-year flirtation with evangelical Christianity, converted by evangelist Ruth Carter Stapleton (sister of President Jimmy Carter) in 1977. He continued to publish his magazine, vowing to "hustle for God," became "born again" and claims he had a vision from God while flying his jet.

During a legal battle related to obscenity in Gwinnett County, Georgia, on March 6, 1978, he and his local lawyer Gene Reeves Jr. were shot outside the county courthouse in Lawrenceville. White supremacist serial killer Joseph Paul Franklin has confessed to the shootings, claiming he was outraged by an interracial photo shoot in Hustler. Franklin, who is serving a life sentence in prison, was never brought to trial. Flynt has made statements indicating he believes Franklin's story, and some law enforcement officials have the same opinion. There remain skeptics, however, so the issue is unresolved. Flynt's injuries left him paralyzed from the waist down, though Reeves recovered more fully. The injury caused Flynt intense, constant pain, and he was addicted to painkillers until multiple surgeries deadened the affected nerves.

After the attack, he renounced Christianity and moved with Althea to a Bel-Air mansion in Los Angeles.

Flynt disowned his eldest daughter Tonya Flynt-Vega after she became a Christian anti-pornography activist. In her 1998 book Hustled, she claims that Flynt sexually abused her as a child. Flynt denies the charges.