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Climate change is exerting unprecedented impacts on marine habitats, and many sessile invertebrate species, such as the endangered giant clam Tridacna maxima, are particularly sensitive to climate driven changes in their environment. Understanding its spatial distribution and conservation requirements is of crucial significance in formulating effective protection strategies. However, the species has been extensively harvested and depleted in many regions, leading to its listing 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. To enhance the management and conservation of this species, we employed a Species Distribution Models (SDMs) approach, integrating occurrence records of T. maxima with environmental variables, to predict its potential distribution based on habitat suitability and capture spatiotemporal changes. Based on geographical and genetic variations, the T. maxima in the Indo‐Pacific core region is primarily divided into two populations: the East Indian Ocean‐South China Sea population (EIOS) and the West Pacific‐Indonesia population (WPI). We first quantified realized niche to reveal significant differences in ecological niche space among different populations. Subsequently, SDMs were constructed at both species and population levels, demonstrating that population‐level SDMs provide more reliable predictions of population distributions due to differential responses to climatic predictor variables. Finally, we conducted an assessment to identify conservation gaps for T. maxima beyond the existing MPAs and proposed recommendations for future establishment of MPAs within the current framework. Based on these findings, appropriate conservation policies have been proposed to effectively protect the habitat of different geographical populations of T. maxima. Additionally, spatiotemporal predictions of habitat suitability provide crucial information for developing adaptive management strategies for T. maxima in response to climate change, including designing new protected areas and adjusting the location and extent of existing protected areas based on their geographical distribution. We employed a Species Distribution Models (SDMs) approach, integrating occurrence records of Tridacna maxima with environmental variables, to predict its potential distribution based on habitat suitability and capture spatiotemporal changes. In addition, we conducted an assessment to identify conservation gaps beyond the existing MPAs and proposed recommendations for the future establishment of MPAs within the current framework. [ABSTRACT FROM AUTHOR]