Chromophoric dissolved organic matter (CDOM) is a significant contributor to the biogeochemical cycle and energy dynamics within aquatic ecosystems. Hence, the implementation of a systematic and comprehensive monitoring and governance framework for the CDOM in inland waters holds significant importance. This study conducted the retrieval of CDOM in Lake Khanka. Specifically, we use the GBDT (R2 = 0.84) algorithm which performed best in retrieving CDOM levels and an empirical relationship based on the situ data between CDOM and dissolved organic carbon (DOC) to indicate the distribution of DOC indirectly. The performance of the CDOM-DOC retrieval scheme was reasonably good, achieving an R2 value of 0.69. The empirical algorithms were utilized for the analysis of Sentinel-3 datasets from the period 2016 to 2020 in Lake Khanka. The potential factors that contributed to the sources of DOM were also analyzed with the humification index (HIX). The significant relationship between CDOM and DOC (HIX and chemical oxygen demand (COD)) indicated the potential remote sensing application of water quality monitoring for water management. An analysis of our findings suggests that the water quality of the Great Khanka is superior to that of the Small Khanka. Moreover, the distribution of diverse organic matter exhibits a pattern where concentrations are generally higher along the shoreline compared to the center of the lake. Efficient measures should be promptly implemented to safeguard the water resources in international boundary lakes such as Lake Khanka and comprehensive monitoring systems including DOM distribution, DOM sources, and water quality management would be essential for water resource protection and government management.