In a filing, managers at the bankrupt firm accuse the couple of holding millions of "fraudulently transferred" dollars and of turning a blind eye to misconduct at the company.
US prosecutors have accused the former billionaire, once dubbed the "King of Crypto", of illegally transferring millions from the exchange to plug losses at his trading firm, make political donations and buy property.
Attorneys for his parents said the claims against them were "completely false" and designed to hurt their son's chances at trial.
The legal action, filed as part of a wider bankruptcy suit, says Mr Bankman-Fried's parents - then both professors at Stanford University - exploited their "access and influence within the FTX enterprise to enrich themselves, directly and indirectly, by millions of dollars".
They received a $10m (£8m) gift in cash from funds that belonged to Alameda, an FTX partner company, while FTX also gave them a $16.4m property in the Bahamas, according to the filing.