Climate change could seriously threaten global lake ecosystems by warming lake surface water and increasing the occurrence of lake heatwaves. Yet, there are great uncertainties in quantifying lake temperature changes globally due to a lack of accurate large-scale model simulations. Here, we integrated satellite observations and a numerical model to improve lake temperature modeling and explore the multifaceted characteristics of trends in surface temperatures and lake heatwave occurrence in Chinese lakes from 1980 to 2100. Our model-data integration approach revealed that the lake surface waters have warmed at a rate of 0.11 °C 10a−1 during the period 1980–2021, being only half of the pure model-based estimate. Moreover, our analysis suggested that an asymmetric seasonal warming rate has led to a reduced temperature seasonality in eastern plain lakes but an amplified one in alpine lakes. The durations of lake heatwaves have also increased at a rate of 7.7 d 10a−1. Under the high-greenhouse-gas-emission scenario, lake surface temperature and lake heatwave duration were projected to increase by 2.2 °C and 197 d at the end of the 21st century, respectively. Such drastic changes would worsen the environmental conditions of lakes subjected to high and increasing anthropogenic pressures, posing great threats to aquatic biodiversity and human health.