In the inverse synthetic aperture radar imaging of ballistic mid-course targets with unsymmetrical appendix parts, the image of the main body may be shadowed by the echo component induced by the unsymmetrical appendix parts. In this paper, the echo model of ballistic mid-course targets with unsymmetrical appendix parts is established, and the micro-Doppler difference between the main body and the appendix parts is analyzed. Then, an algorithm utilizing the Complex-value Empirical Mode Decomposition (CEMD) is proposed to separate the echo of the appendix parts. The echo component of the main body and the appendix parts can be separated and reconstructed with the proposed algorithm adaptively. The results of the simulation verify that a much better image of the main body can be obtained after the separation.