Traditional Fourier transform often apply to analyze and process stationary signals, however, it is weak for time-varying non-stationary signals, and fractional Fourier transform (FRFT) can better solve such problems. The FRFT can be comprehended as the expressive methods on the fractional Fourier domain constituted by the spinning coordinate axis of the signal anticlockwise about the origin at arbitrarily Angle in the time-frequency plane. In this paper, the improved fractional Fourier transform is combined with other calculation methods to achieve high precision estimation of chirp signal parameters. And the communication system built on weighted fractional Fourier transform and discrete fractional Fourier transform is studied and simulated respectively, which verifies the feasibility and improves the anti-jamming and anti-interception ability of the communication system.