The numerical simulation of flow-induced structures is important for the flow analysis of complex fluids. Several schemes have been proposed for coupling the macro-flow computation and the microsimulation of the inner structure of complex fluids. In the present study, the flow-induced structure of star polymers was numerically simulated using a coupling method of multi-particle collision dynamics (MPCD) and coarse-grained molecular dynamics (MD). The polymers were modeled as elastic dumbbells, which consist of finitely extensible nonlinear elastic springs and beads. The motion of the beads was computed by MD. The MPCD was applied to model the effect of Brownian motion and hydrodynamic interactions among the beads. In the present study, the MPC-AT+a algorithm was employed for the collision steps in MPCD computations. The behavior of linear polymers in a shear flow was numerically analyzed to confirm the validity of the present simulation scheme. The numerical results agree well with both experimental results and predictions by other numerical methods. Furthermore, the simulation of star polymers under shear flow was carried out. The present simulation captured characteristic behaviors such as the configuration of the star polymers, which was more compact for polymers with more arms due to extruded volume effects, polymers tumbling at high Weissenberg numbers, and the fluctuation in expansions in the direction of flow decreasing for polymers with more arms.