The effects of periodic spectral modulation on self-similar amplification systems of femtosecond pulses were studied by numerical simulation. Femtosecond pulses with spectral modulation amplified in self-similar amplification theoretical model were simulated, by which the impacts of variables of seed pulses, such as arbitrary phase shift, modulation depth and period, on output results were analyzed. According to the simulation, arbitrary phase shift changes modulated spectral shape, but temporal results of self-similar amplification will not be affected. Besides, large modulation periods make sub-pulses inseparable from main-pulses, disturbing the self-similar amplification process, while small modulation periods bring a longer delay for sub-pulses, making the amplification of main- and sub-pulse independently. This conclusion is still tenable when modulation depth changes.