This paper, taking Chagan lake as the study area, uses and improves MWR V1.0 (Rivers (Lake) Health Assessment Indicators, Standards and Methods V1.0) relating to the theory and method of physical structure integrity assessment. A 500 m × 1000 m grid on the lakeshore zone is a basic evaluation unit, and then a lakeshore physical structural integrity evaluation system using remote sensing (RS) and geographic information system (GIS) technology is established, which contains a target layer, criterion layer and indicator layer. The criterion layer consists of lakeshore condition, shoreline development rate and lake atrophy rate, and the index layer is composed of slope, vegetation cover rate and water level change rate, and another eight indicators. The results showed that for the 23 monitoring points in Chagan lake and the 15 monitoring points in Xinmiao lake, the evaluation results based on RS were 0.60-0.74 and 0.35-0.52, respectively, and the field evaluation results were 0.64-0.77 and 0.35-0.55, respectively. The evaluation results of the two methods consistently indicated that the physical structure of the lakeshore of Chagan lake was healthy and the Xinmiao's lakeshore was sub-health. On this basis, a piecewise evaluation method of physical structure integrity based on the division of the nature reserve function was proposed in this paper.