The expansion of the global tourism market has accelerated the development of small tourist islands. The rapid growth of tourist scale and activity intensity poses a potential threat to the fragile ecosystems of small islands. This article focuses on the ecological stresses small tourism islands face in their development. Compared with similar studies, we found a more flexible way to measure ecological stress of current activities. We show a framework for ecological stress assessment on small rural islands and illustrate it with Weizhou Island, China. It reveals a new approach to combining ecological footprint, geographic data, and visitor activity data. This combination enables a spatial linkage between biophysical and social surveys. To verify the validity of the assessment framework, we assessed the spatial distribution of ecosystem loss on the island using habitat quality. A multi‐scale geographically weighted model describes the spatial correlation between ecological stress and habitat quality. Real‐world application cases were used to test the usability and practical use of the policy assessment framework. We provide methodological and application‐based contributions to support the sustainable development of small tourist islands. Overall, the assessment framework offers a reliable solution for systematically collecting, analyzing, and reporting ecological stresses faced by small tourist islands.