This paper sheds light on the effect of combination modes on the evaluation of berthing capacity for Sanya Yazhou Fishing Port (SYFP) under hypothetical typhoon conditions. By statistically analysing the maximum probability of moving speeds and directions of historical typhoons passing through the fishing port, the representative typhoon path was determined with the nonparametric regression method. The designed typhoon wind fields of levels 12–17 were generated based on Holland’s parametric wind model. Then, the MIKE 21 BW model was used to obtain the high-precision wave distribution in the fishing port. The boundary conditions (significant wave height and peak period) of the MIKE 21 BW model were calculated by combining the MIKE 21 SW model with the designed typhoon wind fields. In SYFP, ships usually adopt the modes of multi-ship side-by-side and single anchor mooring during typhoons. In fair weather, approximately 158 vessels can be berthed if they are all large ones, while approximately 735 vessels can be moored if they are all small ones. However, with an increase in typhoon levels, the anchoring area for small vessels decreases. From the perspective of wave distribution in the fishing port, the number of large vessels moored was hardly affected by typhoons. This can be attributed to the breakwater, which significantly decreases the large wave height in the fishing port. Finally, a study on the framework of a method for hazard assessment of berthing capacity in the coming typhoon-driven storm waves was set up.