Aimed at the problems that the security is not high and the interception is easy, this paper proposes a new kind of satellite antiinterception communication system based on weightedtype fractional Fourier transform (WFRFT) and Multiple Input Multiple Output (MIMO) technology. The system is to modulate the signal by adopting multiple layer WFRFT. The number of WFRFT layers and the transmit antennas is the same. The modulation parameter of each WFRFT layer is different. The original signal subject to WFRFT modulation is characterized as time and frequency domain, can effectively resist the parameter scanning, and MIMO can effectively improve the spectrum utilization and system capacity. By theoretical analysis, the WFRFTMIMO communication system can be used to restore the original signal efficiently, and the eavesdropper can’t intercept the signal. Taking twotransmission and onereception antennas as an example, the results of the contrast of bit error rate (BER) performance between legal receiver and eavesdropper and relationship between receiving performance and WFRFT order deviation are simulated respectively. When the modulation order error of the eavesdropper is 0.1, and the signaltonoise ratio is 20 dB, the BER of eavesdropper is 10-3, which is more than the legal receiver 4 dB. The performance between different receiving performance and transmitting antennas groups is simulated, when the signal to noise ratio (SNR) is 10 dB, the performance of the three transmit four receive antennas is higher than that of the two transmit one receive antennas, which increases the 4.5 dB.