Shallow water model was employed to approximate the three-dimensional flows of a thin micropump to a two-dimensional thickness-averaged flows. The finite element method and pressure correction algorithm were used to solve the twodimensional flows of the pump and calculate the pump flow rate. The numerical results indicate that: 1 ) Phase differences in time of flow velocities and backflows occur across section of diffuser connecting to pump chamber; 2 ) A pair of symmetric vortexes appear inside the pump chamber at the end of suction flow phase; 3) The directional flow rate of the pump is dominated by nonlinearity of Navier-Stokes equations.Quantitative relations of the pump flow rate versus the ratio of diffuser length to width,the ratio of diffuser thickness to width, fluid viscosity and backpressure were also given. Possibly maximal flow rate can be achieved by optimizing the pump parameters.