In this paper based on the pseudo stable seepage theory and mathematical model for numerical simulation of water-oil two phase reservoir, and considering the influence of start-up pressure gradient, a inner boundary conditions is derived, in which three cases were considered: fixed flow pressure, fixed oil production rate and fixed liquid production rate. Then, by means of full implicit finite difference scheme, the corresponding numerical model is established and solved by pretreatment conjugate gradient method. The simulation results show that, in inner boundary conditions, the start-up pressure gradient obviously affect flowing pressure of wells. In case of fixed oil production rate, with the increase of start-up pressure gradient, the flowing pressure becomes lower.