The pedestal components in output signals of spatial filtering velocimeter can be completely eliminated by differential method theoretically. However, because of varying amount of radiation energy incident onto the photodetector, some pedestal components still occur in the output signals, making it difficult to pick up desired signals, especially signals having very low frequencies close to zero. To remove the pedestal components in output of differential filters, the configuration of a COMS-type differential spatial filter in spatial filtering velocimeter was optimized. Every possible configuration of a differential filter was listed, and several typical configurations were chosen to analyze in detail by carrying out experiments. The quality of the output signals were analyzed in the aspects of power spectrum and signal-to-noise ratio under the condition of uniformed and non-uniformed illumination respectively. By comparison of quality of output signal from these several typical spatial filters, a most suitable configuration was obtained. This optimized configuration can noticeably eliminate the pedestal components in output signals.