The invention discloses a communication receiver anti-interference method on the basis of blind signal separation and a system thereof, wherein the method comprises: utilizing a positive-negative 45 degree dual polarization antenna module to receive signals, changing a two way high frequency signal into an intermediate frequency analog signal, outputting an intermediate frequency digital signal by the intermediate frequency analog signal through analogue/digital conversion and after an orthogonal transformation module, then, carrying out digital down conversion, abstracting, filtering, and the like, transforming into a DSP baseband complex signal, obtaining a statistical independent signal after two ways are separated by the complex signal after passing through a linear blind signal separation algorithm module, carrying out self-adaptive equalization processing to a two way estimating signal after blind separation, counteracting crosstalk in a communication channel, utilizing a known modulation and demodulation method to demodulate a two way independent signal, analyzing a two way signal, and abstracting a useful signal. The invention does not need to use any other reference signals, adopts the linear blind signal separation algorithm to estimate the two way independent separation signal, the calculation complexity is low, and the disturbance to the communication receiver under the condition of low signal-to-noise ratio can be eliminated.