Reg Traviss, 35, faces two counts of rape and will appear before magistrates next month.
He had been seeing the singer for more than a year when she died at her home in Camden, north London, last July.
The film director has been behind movies including Psychosis, which featured Charisma Carpenter and Darkness frontman Justin Hawkins.
Reg Traviss, who was charged under his full name Reginald, was arrested on April 5 by the Metropolitan Police in relation to an allegation of rape reported on January 18.
Rebecca Mundy, a lawyer for the Crown Prosecution Service, said: “I have authorized the Metropolitan Police to charge Reginald Traviss with two counts of rape.
“The alleged offences took place between 29 December 2011 and 1 January 2012.”
The lawyer from the CPS London Rape and Serious Sexual Offences Unit added: “The decision was taken in accordance with the Code for Crown Prosecutors.”
Reg Traviss will appear at Westminster Magistrates’ Court on July 17.
Last year, Reg Traviss revealed him and Amy Winehouse, who died aged 27, had been planning to get married.
He admitted that he still hadn’t come to terms with the fact she has gone.
Speaking to the Sunday Times, Reg Traviss said: “What felt surreal was not the cameras and the craziness but losing somebody, just like that. One minute I was speaking to her, the next she was gone.
“You might say we were halfway through a conversation in our life together and then, suddenly, she disappeared.”
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