The invention discloses a communication radiation source individual identification method and system. According to the technical scheme, the method comprises the steps of: receiving communication radiation source signal, carrying out radio frequency preselection amplification, carrying out frequency mixing, carrying out intermediate frequency filtering, carrying out A/D conversion, carrying out digital orthogonal demodulation, carrying out rectangular integration double-spectrum transformation, dividing rectangular integration double-spectrum characteristic vectors into a training sample set and a testing sample set, constructing a rectangular integration double-spectrum characteristic dictionary, carrying out non-linear transformation, carrying out mapping to a cooperation projection matrix, constructing a classifier, obtaining classification residual errors, and using the type corresponding to the smallest classification residual error as type of a communication radiation source individual. According to the invention, a small sample problem in a communication radiation source individual identification process is solved, the time complexity of the algorithm is lowered, and the phase and amplitude information distortion problem in the process when an existing method based on the time domain, frequency domain or time frequency domain is used to process non-stable or non-Gaussian signals is adopted.