In this study, a simulation program was developed, which could simulate a fuel injection system for low-speed marine diesel engine. The fuel injection system was divided into fuel injection pump, high pressure pipe and fuel injection valve. The unsteady flow in the high pressure injection pipe was analyzed by the method of characteristics, considering cavitation and variation of fuel density and bulk modulus. It was confirmed that the simulation results were good agree with experimental results of injection pressure and quantity at the high pressure distributor in fuel injection system for the training ship "M/V Hannara". And the effects of the atomizer hole diameter, maximum needle lift, plunger diameter and nozzle opening pressure were also investigated with simulating results.g results.