Spectral clipping effect in a chirped pulse amplification laser system is developed in this paper. A grating-size-limited stretcher/compressor as well as an amplifier can alter the spectrum profile of an ultrashort pulse, so the temporal profile will be influenced. We present a model of spectral clipping effect and calculate the wavelength-dependent spectral clipping ratios in a CPA laser system for a variety of matched stretcher-compressor designs. Then we analyze the output pulse’s temporal distribution, and find that the temporal contrast ratio is mainly determined by the stretcher and the amplifier. The pulse duration of the output pulse is mainly influenced by the amplifier.