If a traditional explicit numerical integration algorithm is used to solve motion equation in the finite element simulation of wave motion, the time-step used by numerical integration is the smallest time-step restricted by the stability criterion in computational region. However, the excessively small time-step is usually unnecessary for a large portion of computational region. In this paper, a varying time-step explicit numerical integration algorithm is introduced, and its basic idea is to use different time-step restricted by the stability criterion in different computational region. Finally, the feasibility of the algorithm and its effect on calculating precision are verified by numerical test.