Considering the characteristic of long transmission delay in Geosynchronous Orbit(GEO) satellite communication system, it is very important to put forward an applicable resource scheduling algorithm for GEO satellite Long Term Evolution(LTE) system. Based on the Modified Largest Weighted Delay First(M-LWDF) algorithm, a cross-layer scheduling algorithm is proposed with the comprehensive consideration of parameters in the Media Access Control(MAC) layer and application layer for enhancing the efficiency of resources allocation. Specifically, a greater weight delay factor is put forward from the point of mathematical deduction in the MAC layer, in addition to introducing Q factor into the application layer according to service priorities. Comparing with M-LWDF algorithm, the simulation results show that the cross-layer based resource scheduling algorithm can reduce transmission delay and improve the throughput for different traffics, whereas fair performance decreases slightly and the complexity increases.