Coordinated Multi-Point (CoMP) transmission is considered as a tool for 3GPP LTE-Advanced to increase the cell edge throughput. In CoMP JT (Joint Transmission) mechanism, multiplied time-frequency resources are occupied by JT users. Additionally, scheduling relevancy exists among the users, i.e., scheduling orders of different users influence on the cell average and cell edge throughput. So the impact of scheduling relevancy should be considered among the users in the same coordination cluster. Otherwise, the CoMP system throughput will decline significantly. To address this issue, an effective scheduling scheme is proposed for CoMP in heterogeneous scenario. Taking both the user fairness and the throughput of the coordination cluster into account, a suitable scheduling scheme is proposed to improve the system throughput. System-level simulation results prove that, the proposed scheduling scheme outperforms the conventional scheduling scheme in terms of both cell average and cell edge spectral efficiency.