A fast recognition and acquisition algorithm of the received signal of the satellite-based direct sequence spread spectrum/phase modulation(DS/PM) dual-mode transponder is put forward and the performance of the algorithm is analyzed. Compared with the traditional method, the algorithm improves the system performance, optimizes the system structure and reduces size of the hardware requirements by multiplexing the common processing unit(FFT/IFFT). The contradiction between the acquisition speed and detection performance with the high dynamic, low SNR and large Doppler shift is resolved. This research will be useful to the development of DS/PM dual-mode transponder.