Due to the compact spatial structure of missiles and the close proximity between antennas of different wireless communication device, the electromagnetic compatibility problem of multi-antenna systems is becoming increasingly prominent. To solve this problem, this paper establishes an electromagnetic simulation model comprised of missile, two inverted-F antennas, microstrip antenna and microstrip array antenna, which is based on the numerical simulation software CST. In order to evaluate the electromagnetic compatibility between antennas in the multi-antenna scenario, the S parameters representing the coupling degree between antennas are simulated and solved. The simulation results show that the coupling transmission parameter between two inverted-F antennas are much higher than other antenna pairs, which indicates the antenna coupling degree is closely associated with the distance between antennas and the structural form of the antenna. Further, a method for evaluating the electromagnetic compatibility of multi-antenna system is presented, and a calculating method for the suppression performance indexes of the antenna radio frequency filter is provided.