The Isle of Man Met Office predicts wind speeds could reach up to 55mph (88km/h) later and on Thursday.
The 08:45 GMT sailing between Douglas and Heysham and the 14:15 are affected, the Isle of Man Steam Packet Company said.
A spokesman said the 19:45 and overnight service could also face disruption or cancellation.
Affected passengers have been asked to contact the company.
The Met Office has issued a yellow warning for cold and windy weather on Wednesday, Thursday and Friday, with a "likelihood of hail, snow and temperatures close to zero".
It has also issued a flood warning for Peel promenade at high tide at 10:15.
Strong winds have led to the cancellation of two ferry crossings between the Isle of Man and Lancashire.