A numerical simulation method is presented in this paper for 3D low speed micro flapping-wing with complex kinematics. The main characteristics for the numerical simulation of Flapping-wing Micro Air Vehicle (FMAV) include: low speed, big range of wing motion, and complex kinematics. The low speed problem is solved by preconditioning method. The big range of wing motion problem is solved by chimera grid system. The problem of complex kinematics is solved by decomposed into three main motions, i.e. plunging, pitching, and swing respectively. The numerical method is solving the Reynolds Averaged Navier-Stokes equations for the viscous flow over micro flapping-wing. The numerical method of this paper is validated by good accordance with experimental results of reference. This method can used to simulate the aerodynamic performance of micro flapping-wing with complex kinematics in low speed and is helpful to the FMAV designers as a design tool.