Frequent typhoons pose significant challenges to the safe mooring of fishing vessels along the coastal regions of China. This paper investigates the dynamic response and interaction of fishing vessels moored side by side in a harbor under typhoon conditions using numerical simulation methods, assessing the safety of the mooring system. A model of side by side anchored of fishing vessels is established using AQWA software to analyze the effects of different mooring schemes on the roll and pitch motion responses of the fishing vessels, the tension in the bow anchor chain, the force on the fender, and the tension of the connecting cable between the fishing vessels. The results show that when fishing vessels are moored side by side in the harbor, the outermost fishing vessel experiences the largest roll motion response, while the middle vessel has the smallest. Increasing the number of anchor chains reduces the average tension, with each anchor chain bearing the same tension under different anchoring schemes. The variation in the tension of the connecting cable between the fishing vessels exhibits an opposite trend to the variation in the force on the fender. For safety and economic considerations, adding anchor chains to the middle vessel is the preferred mooring method.