Considering the limited antenna size, limited repeater power and other characters of the space-based Phased Array TT&C Communication Satellite, this paper presents a new calibration method called "PN sequence +non-data BPSK", which guarantees the accuracy of channel amplitude and phase calibration by combining with Multi-period Coherence Accumulation under the condition of low SNR. The result of simulation experiment shows that Low Probability Intercept and Anti-jam Protection are the characters of this new technology.