Multi-machine coordination is a crucial issue to obtain high working rate and trajectories of collision avoidance in the dynamic compact environment for high-speed press line. This paper proposed a method based on simulation in MATLAB to coordinate multiple machines in auto-body-panel stamping line and verify the correctness of simulation results simultaneously. The proposed method consists of variable-period phase delay and minimum safe distance based on Dijkstra algorithm, which are used to achieve multi-machine coordination and collision avoidance, respectively. MATLAB-ADAMS co-simulation of auto's side-frame outer panel has been taken as an example to illustrate and confirm the efficiency of the proposed method. Meanwhile, the optimal results obtained from the proposed method are better than the previous simulation results under the same technical requirements. In addition, the proposed method combines programming with simulation in MATLAB, which can verify results timely and provide a guide for presenting the status of high-speed press lines at one moment in the graphical user interface.