Based on the direct coupling structure of two-dimensional square lattice phononic crystal filter, the influence of location and size of point defects on the transmittance of phonon crystal were studied, thus the optimal phononic crystal filter was designed. Using the FDTD method, the effects of point defects on the transmittance of filter were discussed by the simulations performed with COMSOL software. It is concluded that when the location of point defects of direct-coupling phononic crystal filter is in the middle of line defect and the filling factor of media column at point defects is 0.0228, the transmittance can achieve 92%, meeting the design demand.