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Due to the limited bandwidth usage of wireless transmission, one of the major research topics is how to make a higher system throughput to support the multiple users based on limited bandwidth resources. This paper proposed a cross-layer subcarrier permutation mechanism (CLSP) and designed the service scheduling in the IEEE 802.16e system. The simulation results showed that when the throughput of system transmission become completely in use, the throughput of cross-layer proportional fair subcarrier permute mechanism is 28 percent more than the throughput of PUSC (Partial Usage of sub-channels) model formed by the IEEE 802.16e committee. In the user capacity, the number of users of cross-layer proportional fair subcarrier permute mechanism is 17 percent more than the number of users of PUSC. Moreover, cross-layer proportional fair subcarrier permute mechanism has a lower delay time as well as a long-term fairness among different users during the different service flows simulation.