In order to study the effect of mismatched spacing and angle of zero-dispersion femtosecond pulse shaping system on the temporal properties of the output femtosecond pulses, the relation between the resolution and the mismatched spacing of the system was analyzed in theory. And then the effect of mismatched spacing and angle on the system efficiency and the width of the output pulses were discussed. The experimental results indicated that lens misalignment can broaden the pulse, and the influences of the first and the second gratings are symmetrical. Moreover, the influence on system efficiency of angle misalignment was more serious than spacing misalignment. If 600 lines per millimeter grating and lens of 30 centimeter focal length were used, when the angle misalignment was smaller than 9°and spacing misalignment was shorter than 0.5 centimeters, the changing of system efficiency and pulse width were both smaller than 5%. All the results above are helpful to an in-depth study on the zero-dispersion pulse shaping system.