Underwater trajectory is a unique trajectory of submarine-launched cruise missile different from other kinds of cruise missiles. Although time is short, the missile has undergone changes in complex environment. It has been affected mainly by waves and streams during moving. Focused on the process and characteristics of underwater vertically launched missile, the model of underwater motion was established, and according to the theory of average wave and the Morison equation, the model of the currents and waves was established. By simulation, it makes a conclusion about the change of attitude and locus of missile in different course and sea condition, which provides a reference for studying underwater trajectory of cruise missile.