In order to suppress the non-characteristic harmonics in shipboard medium voltage power system caused by single phase grounding fault, the influence of neutral grounding mode of the 6-phase generator with rectifier-load on the harmonics is studied. Firstly, the switching function and method of symmetrical components are used, the calculation methods of characteristic harmonics at normal situation and non-characteristic harmonics in fault situation of DC voltage are obtained respectively, then the harmonics expression of AC fault current is deduced by using DC voltage. Secondly, the zero-sequence loop in fault is analyzed, and the relationship between grounding resistance and non-characteristic harmonics of DC voltage is obtained, and the influence of grounding mode on harmonics is analyzed. Finally, the conclusions are verified by simulation software PSCAD/EMTDC and experiments. The obtained results provide a basis for the selection of grounding mode for shipboard medium voltage power system. This work is supported by National Natural Science Foundation of China (No. 51607184).