A modern pulse radar uses more and more complex waveforms. Some waveforms are developed intentionally to make their interception almost impossible or jamming resistant. The main distinctive features of radar signal are hidden in its intra-pulse structure. The intra-pulse modulation analysis of a detected signal is the major task of ELINT/ESM systems, too. As a result of measurement, for each pulse specific description, so called finger printing, containing primary parameters, is created. Determination and decomposition of signal in case of M-ary Frequency Shift Keying intra-pulse modulation (M-FSKIM) in the recent hardware implementation of ELINT receivers is difficult to achieve. In this paper, the principle of unknown radar signals with M-FSKIM decomposition by new approach in signal analysis is described. The proposed method is based on subspectral decomposition method. The subspectral decomposition method principle and results of modeling and simulation of M-FSKIM signal processing and decomposition are presented.