The current equivalent linearization method for evaluation of seismic response of soil layers has been widely used by engineers, but it obviously has limits while considering severe earthquake action and dealing with extremely soft soil layers. Developing a direct time-domain integral method is essential. In this paper, a direct-domain integral method is proposed. In the method, the dynamic skeleton curve constitutive model is introduced and it can fit test results of dynamic shear modules ration curve and damping ratio curve simultaneously, central difference integration method is used to solve the dynamic equation, multi-transmitting artificial boundary condition has been conducted to consider the effect of energy transmission through bedrock boundary. In order to implement this method, a program called Dymatlab has been compiled, strong motion records got from the NGA data base for site effects on strong ground motion have been used to analysis the offshore engineering site with thick soft soil layers. The results show that this program can be applied as a reasonable and feasible method for nonlinear seismic response of soil layers.