To solve the problem of local remeshing in multi-body separation numerical simulation of flight vehicle with unstructured mesh, a method for the construction of local remeshing regions was proposed based on element neighbouring indices. Firstly, the mesh quality was checked by the element radius ratio and the remeshing regions were marked. Secondly, the remeshing regions were extended by the neighboring indices of mesh elements. Finally, the around elements of the non-two manifold sides were marked for ensuring the boundary definition of remeshing regions which satisfied two sides manifold criterion. The numerical experiment of a separation simulation was conducted by the proposed method. In this simulation, the local remeshing was operated successfully for 16 times, and the average of the overall remeshing element radius ratio was improved above 0.71. The calculation results and comparative analysis of the wind tunnel experimental data shows that, the trajectory and motion of the separation were calculated accurately in the numerical experiments. It is verified that the proposed unstructured remeshing process is effective.