The signal collected by a non contact physiological signal monitoring system should be separated fast and accurately in real time. In this paper, the fast complementary ensemble empirical mode decomposition (FCEEMD) was used for the physiological signal processing, in which white noise was added in pairs into the original signal and the empirical mode decomposition (EMD) was used to obtain a series of intrinsic mode functions（IMFs）. The separation of the original signal was realized, a fixed iterations time of sifting to the stoppage criterion is used to ensure that the algorithm is fast in realtime. By analyzing the simulation and actual signals, the results show that the algorithm can solve the modemixing problem effectively and obtain heartbeat and respiration signals accurately and quickly.