Chromophoric dissolved organic matter (CDOM) in aquatic environments is an important component of the biogeochemical cycle and carbon cycle. The aim of this study is to investigate the long‐term changes in CDOM in shallow and eutrophic Chaohu Lake, as well as its relationship with climate, environment and social factors. Using long time series Landsat image data and machine learning technology, the spatiotemporal evolution of Chaohu CDOM since 1987 was reconstructed. A total of 180 samples were collected, which were divided into three parts based on regional and hydrological characteristics. The results show that the water quality in different regions were significantly different, and TN may be the key factor driving the change of CDOM in Chaohu Lake. Machine learning algorithms including random forest (RF), support vector regression (SVR), neural network (NN), multimodal deep learning (MDL) model and Extreme Gradient Boosting (XGBoost) were used, among which XGBoost model performed best (R2 = 0.955, mean absolute error [MAE] = 0.024 mg/L, root mean square error [RMSE] = 0.036 mg/L, bias = 1.005) and was used for CDOM spatiotemporal variation retrieval. The change of CDOM was seasonal, highest in August (0.67 m−1) and lowest in December (0.48 m−1), and the western lake is the main source of CDOM. Annual variability of the CDOM indicates that it began to decline after the completion of water pollution control in 2000. Temperature changes were closely related to CDOM (P < 0.01) and agricultural non‐point source pollution plays an important role in Chaohu Lake. This study will provide feasible methods and scientific basis for the long‐term remote sensing supervision of CDOM.