The adult population of tri-spine horseshoe crabs (Tachypleus tridentatus) in Taiwan has been considered nearly extinct for decades, resulting in its exclusion from data moderation assessments in previous studies. This highlights a significant gap between historical baseline data and recent research efforts in the Taiwan Strait. In this study, the population size was estimated using five years of mark-recapture data and identified potential habitat to simulate suitable habitats through the MaxEnt model. This is the first comprehensive assessment of the adult T. tridentatus population in the Taiwan Strait in decades. The result of the population size of T. tridentatus was estimated to be approximately 64,243 individuals in Taiwan. Habitat predication was identified not only the well-documented inshore where function was breeding and nursery areas critical for juveniles but also highlighted central strait regions, including the Taiwan Bank and Changyun Ridge, as high probability of occurrence for potential adult foraging ground with that may been overlooked in the historical baseline data. These findings indicated that the importance ecological niches of the Taiwan Strait for T. tridentatus, functioning as a breeding ground, conservation zone, foraging area, and migration corridor that connects Taiwan and the eastern coast of China. Based on these results, we propose a regional conservation strategy emphasizing international collaborative monitoring, cross-border conservation measures, the implementation of conservation practices, and benefit assessments. This work provides valuable insights for developing and implementing an action plan for the conservation of Asian horseshoe crabs.