The rolling motion of ship with water on deck is studied by the numerical method. The model for quality of water on deck is set up based on the corrected Bernoulli equation. The formulas of center of gravity and height of water on deck are derived according to the different cross section of water on deck. The rolling equation of ship is established with considering the heeling moment due to the trapped water on deck. Taking a stern trawl ship as an example, the roll ing responses of ship for different initial water on deck, wave frequency and wa ve height are calculated, and the effect of trapped water on deck to ship rolling is investigated. It is found that the amplitude of rolling response of ship is increased greatly by the water on deck when there is some initial water trapped on deck and the frequency of wave is relative low.