Shale gas reservoir is abundant in nanoscale pores. Therefore，the gas seepage is influenced significantly by slippage effect. Conventional flow model cannot simulate the seepage law accurately in shale gas when gas flows in nanometer pores. In order to improve the accuracy of production simulation and make guidance for fracturing operation in the shale gas reservoir，slippage effect during gas flow must be analyzed precisely and directly. Lattice Boltzmann method was applied to built seepage model of the shale gas and to know boundary condition of bounceback-specular combination. The slippage effect in the shale gas reservoir was simulated and analyzed. The results show that the pore size and Knudsen number are the decisive factors which can be used to characterize the strength of slippage effect. The slip velocity of the gas molecule along the pore channels has approximate linear growth and increases more dramatically in the outlet end，which can testify the compression effect and rarefaction effect of the gas in the shale gas reservoir. The slip velocity will increase dramatically with the rising Knudsen number，especially after gas seepage in slip zone. The limitation of models based on continuous medium formula will be highlighted. With the rise of Knudsen number，the apparent permeability has been increased sharply. Klinkenberg model is no longer suitable for simulation of slippage effect during gas seepage in slip zone after the Knudsen number is more than 0.1.