The percolation mechanism and regularity for stepped horizontal well in multilayer complex fault block reservoir are complex. A percolation mathematical model based on unsteady flow mathematical model is built up in this paper. In the model, the reservoir couples with one horizontal well in sealed reservoir which perforate through mutually unconnected formation. The model is solved by the methods such as Laplace change, Stehfest inversion and Conjugate gradient. Compared with the result of Saphir method, the model is proved to be of great reliability. As shown in the application of actual reservoir, the model could calculate BHP and production distribution of various production phases accurately. It can provide theoretical foundation of reservoir research engineering and production engineering design for reservoir development with stepped horizontal well in multilayer complex fault block reservoir.