The no-load closing of transformer in the medium-voltage ship power system will cause a large inrush current and threaten the security of the system. This paper aims to provide reference for the pre-magnetization technology of the transformer in medium-voltage ship. Firstly, the basic principles of the inrush current and the series small-capacity transformer based pre-magnetization technology for the transformers are analyzed. Based on the analysis, the typical medium-voltage engineering ship and power generation ship are taken as examples to perform the simulation of the series small-capacity transformer based pre-magnetization scheme, and the result shows that the pre-magnetization technology can suppress the inrush current effectively. Besides, the factors of the switch closing time and the number of generators operating in parallel are considered in the research and their effects of on the inrush current as well as the transient voltage drop are analyzed. Finally, the influence of the pre-magnetization scheme on the differential protection is studied and the operation suggestions are given.