Customers noticed that episode 12 of season 16 is missing from Disney +, which launched in the city this month.
It comes as authorities in Hong Kong clamp down on the entertainment industry, banning films that violate a strict national security law.
Disney has not commented on the missing episode.
The episode, named "Goo Goo Gai Pan", sees the cartoon family visit China.
During their trip to Beijing, they visit Tiananmen Square where a sign reads: "On this site, in 1989, nothing happened" - a nod to censorship of the deadly crackdown on protesters there that year.
The demonstrators were calling for greater political freedom, and soldiers killed many unarmed civilians.
Nobody knows for sure how many were killed. In June 1989, the Chinese government said 200 civilians and several dozen security personnel had died. Other estimates have ranged from hundreds to many thousands.
In another part of the episode, the Simpsons also visit the embalmed body of former Chinese Communist leader Mao Zedong, whom Homer refers to as "a little angel that killed 50 million people".
Mao led China through its Cultural Revolution, and a devastating famine that killed many millions of people.
It is not clear why the episode is missing and who made the decision not to include it on the streaming service. The BBC has contacted Disney for comment.