In mobile satellite communication system, transmission power and frequency band are limited by the satellite inherent characteristic. And spot beam architecture is widely adopted with similar frequency reuse schemes in terrestrial cellular systems, in which the entire spectrum is orthogonally assigned to adjacent beams, resulting in a relatively lower system spectrum utilization. In addition, the beam diffuse effect in the edge deteriorates the situation. Therefore, a new frequency resource allocation scheme for mobile satellite communication system is proposed in this paper. We analyzed the system performance by calculating global frequency reuse factor, system transmission capability and beam unit throughput. Both theoretic and simulation results show that Master-Aide multi-beam architecture is an appropriate compromise between system performance and computing complexity in the GEO satellite mobile communication system.