The influence of oil-based drilling fluid on the geochemical characteristics of source rocks has been widely reported in the northern South China Sea. However, contamination from water-based HEM drilling fluid has long been neglected in previous deep-water petroleum exploration. To further understand the impacts of HEM drilling fluid on deep-water source rocks, the organic matter abundance and type, kerogen maceral composition, and saturated biomarkers of the deep-water source rocks in the Qiongdongnan Basin were investigated. The influence of HEM drilling fluid on the organic geochemistry data of cuttings is significant but minor for sidecores. It is evident that the organic drilling additives in HEM drilling fluid can increase the organic matter abundance and optimize the organic matter types of shale cuttings. Specifically, the total organic carbon, S 1 , S 2 , and hydrogen index are increased by 28.5 ± 6.1, 90.8 ± 2.0, 34.2 ± 2.0, and 51.9 ± 4.0%, respectively. Furthermore, the organic drilling additives will greatly enhance the levels of C 29 regular steranes, especially for C 29 -ααα-20R sterane, with the influence still persisting even when conducting GC-MS-MS analysis. The highly abundant 17α (H) -22, 29, 30-trisnorhopane, 17β (H)-22, 29, 30-trisnorhopane, C 29−31 17α (H), 21β (H) hopanes, and C 29−31 17β (H), 21α (H) hopanes may directly originate from the organic drilling additives. It is dangerous to directly use organic geochemical data from deep-water source rock cuttings contaminated by HEM drilling fluid as it may lead to conclusions that are entirely inconsistent with the basin's geological background.