Population conservation of horseshoe crab is urgently required in China as their population is declining dramatically. However, conservation efforts are severely constrained by the lack of information on the population dynamics of the species. Here, a citizen science-based investigation was conducted to continuously monitor the population dynamics of juvenile Tachypleus tridentatus and Carcinoscorpius rotundicauda in the Beibu Gulf of China over five years. A low abundance of horseshoe crabs was observed at all stations. T. tridentatus was primarily observed in the eastern of Beibu Gulf, with an abundance (0.179 ind/100 m2) larger than that of C. rotundicauda (0.007 ind/100 m2). The prosomal width range of T. tridentatus was between 9.0 and 138.0 mm while that of C. rotundicauda was between 20.0 and 111.0 mm, representing their different age distribution patterns. A continuous distribution pattern from 3rd to 14th instar was observed in the T. tridentatus population, whereas a discontinuous distribution pattern from 6th to 16th instars was observed in the C. rotundicauda population. This instar distribution pattern implies that these areas are crucial nursery habitats for the two species. No horseshoe crab within the 1st to 2nd instars (for T. tridentatus) or before 6th instar (for C. rotundicauda) were observed within five years, indicating a declining age structure with few natural births. It was concluded that the declining population would exacerbate the risk of endangered horseshoe crab. There is an urgent need to strengthen the protection of horseshoe crab in the Beibu Gulf, particularly to protect their nursery habitats. The value of long-term citizen science based-monitoring was highlighted, which greatly increased public awareness of horseshoe crab protection.