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.