Tridacna maxima (T. maxima) are widely distributed in shallow areas near coral reefs and hold significant commercial value as a food source and for marine tourism. However, it has been extensively harvested and depleted in many regions, leading to it being listed as endangered species by the International Union for Conservation of Nature (IUCN). While marine protected areas (MPAs) are considered effective conservation tools, it remains uncertain whether existing MPAs adequately protect these vulnerable giant clams. Here, we employed a Species Distribution Models (SDMs) approach, combining occurrence records of T. maxima with environmental variables, to predict their distribution and capture spatiotemporal changes. The findings revealed the importance of land distance and light at bottom in determining the distribution of T. maxima, with suitable habitats predominantly found in shallow coastal waters rather than deep sea areas. Furthermore, we modeled potential distribution areas for T. maxima in 2050 and 2100 under different climate change scenarios, highlighting varying impacts on suitable habitats across different model predictions. To evaluate current conservation gaps, we conducted an analysis by overlaying suitable areas with existing protected areas. The results showed that the potential distribution area of T. maxima is 1,519,764.73 km2, accounting for only 16.10% of the total protected areas. It became evident that the existing protected areas are insufficiently large or well-connected, suggesting their ineffectiveness in safeguarding giant clams. Therefore, management efforts should focus on establishing a network of MPAs along the coastlines of West Pacific-Indonesia, matching the dispersal capability of giant clams. These findings provide valuable insights for the conservation of endangered giant clams, offering a scientific foundation for designing MPA networks in the Indo-Pacific region.