Horseshoe crab has high economic and scientific values. In recent years, because of overfishing and habitat degradation, the population of horseshoe crabs in China is decreasing rapidly. However, their long life cycle makes it extremely urgent to protect horseshoe crabs. Ecological niche models have been widely applied to predict the potential geographic distribution of species. The habitat suitability index of the Chinese horseshoe crab Tachypleus tridentatus and mangrove horseshoe crab Carcinoscorpius rotundicauda in the Beibu Gulf (Chinese part) was determined by using the maximum entropy model and the distribution of habitat suitability of the two types of juvenile horseshoe crab in the Beibu Gulf was determined based on field survey data and published data on the geographical distribution of two horseshoe crab species in the Beibu Gulf. The model analysis results showed that the slope of the intertidal zone and topographic index were the main environmental factors affecting the distribution of the Chinese horseshoe crab, while the organic content and vegetation index of intertidal sediment were the main environmental factors affecting the distribution of the mangrove horseshoe crab. According to the results, to promote the recovery and development of horseshoe crab resources, protected areas should be established, artificial release of juvenile horseshoe crabs in habitat suitability areas of horseshoe crab should be conducted, and the ecological construction of seagrasses and mangroves in these areas should be strengthened.