The 83-year-old director is seeking $68m (£52m) from Amazon Studios, accusing the company of breach of contract.
The lawsuit said Amazon knew about a “25-year-old baseless allegation” before signing with Allen in August 2017, but still used it as an excuse to back out of the deal.
Allen claimed Amazon refused to release his completed film A Rainy Day in New York and abandoned a four-movie production and distribution arrangement.
According to the lawsuit, the company pulled out of the deal last June after an accusation resurfaced that he had molested his adopted daughter Dylan Farrow in 1992.
The filmmaker’s complaint said: “Amazon has tried to excuse its action by referencing a 25-year-old, baseless allegation against Mr Allen, but that allegation was already well known to Amazon (and the public) before Amazon entered into four separate deals with Mr Allen.
“It does not provide a basis for Amazon to terminate the contract.”
Allen, who has won four Oscars, has repeatedly denied the allegation by Dylan Farrow and her mother Mia Farrow, who was Allen’s long-time partner and starred in several of his movies.
Allen said prior to abandoning the movie agreement, Amazon had become concerned about fallout from the #MeToo movement.
It allegedly feared “negative publicity and reputational harm” over its links to disgraced movie mogul Harvey Weinstein and harassment claims against its former president Roy Price.
Allen’s submission included two emails from Amazon lawyers, one of which referenced “renewed allegations against Mr Allen, his own controversial comments, and the increasing refusal of top talent to work with or be associated with him”.
Amazon first signed Allen in 2015, leading to the widely-criticised Crisis In Six Scenes, followed by 2017’s Amazon-produced Wonder Wheel, starring Kate Winslet and Justin Timberlake.
The four-movie contract was then signed but the relationship soon ran into trouble.
Allen said he agreed to delay the release of A Rainy Day In New York, his latest movie, only to have Amazon Studios cancel their contract altogether, leaving the film in limbo.
Ms Farrow renewed her sex abuse accusations against Allen in an article headlined “Why has the #MeToo revolution spared Woody Allen?” in the LA Times in October 2017.
It prompted a number of Allen collaborators to disown the director and films they had made with him.
Timothee Chalamet, who starred in Rainy Day, donated his salary to charity, saying: “I don’t want to profit from my work on the film.”