Water–land ecotones (WLEs) of lakes are key regulators of the carbon cycle and climate dynamics, playing a pivotal role in both terrestrial and aquatic ecosystems. Structural information on surface water, such as patch number and morphology, is essential for lake restoration and biodiversity conservation. However, such structural information remains limited for China’s major freshwater lakes. This study assessed the spatiotemporal variations in total area (TA), patch number (PN), and the structure characteristics of surface water bodies of different sizes in China’s three major freshwater lakes (WLEs) from 1990 to 2023, and examined the impacts of key driving factors. We found that TA in Dongting Lake and Poyang Lake experienced substantial losses, whereas Taihu Lake exhibited recent recoveries. PN trends in the three lakes showed relatively minor fluctuations, they declined over time. Moreover, changes due to reclamation, and the implementation of Yangtze River protection policies significantly influenced the surface water structure of the lakes’ WLEs. Our findings provide critical insights for policymakers and stakeholders seeking to address the growing challenges of ecosystem restoration, governance, and sustainable development in the WLEs of China’s major lakes.