A spectral scanning filter method to improve the pulse contrast in the femtosecond chains is proposed, which is made using of the character that the instantaneous frequency varies with the time approximately linearly for the chirped pulse in the time-frequency domain. A spectral scanning filter based on the bi-refraction electro-optical interferometer is proposed and analyzed. The spectral scanning filter for reducing the ASE intensity is analyzed in the time–frequency domain by using the Short-Time Fourier Transformation method. The results show that the pulse contrast can be improved by two orders, and the transmission efficiency of the chirped pulse can exceed 85% when the synchronizing time jitter ranges from −50ps to 50ps adopting the cascaded filter method. The great advantage of this novel nonlinear spectral filter technology fits the high energy and high peak intensity femtosecond chains for it filters the ASE in the near field in temporal domain.