Abstract: In order to reveal the geochemical characteristics of trace elements in marine surface sediments in Guangdong-Macao in-depth cooperation zone in Hengqin, the authors analyzed the grain size of surface sediments and 14 trace elements. The distribution, source and control factors of trace elements in surface sediments were discussed, combined with element correlation analysis and factor analysis, and the potential ecological risk of heavy metal elements were evaluated. The results are as follows. ① There are five types of surface sediments in the cooperation zone, including sand (S), muddy sand (mS), sandy silt (sZ), silt (Z) and mud (M). ② The content of Zn, V, Cr and Ba in surface sediments of the cooperation zone is relatively high, with an average of more than 100×10^-6. The content of Ba is the highest with an average of 431.13×10^-6, and content of Cd is the lowest with an average of 0.73×10^-6. The average content of other elements is between 15.95×10^-6 to 83.03×10^-6. The surface sediments in the cooperation zone are enriched in the heavy metals, such as Cd, Pb, Zn, As, and Cu, compared with the sediments in Pearl River. ③ Natural weathering of land rock and artificial discharge are the main source of the trace elements in surface sediments of the cooperation zone. The content variation of Sc, Co, Ni and Ga are mainly controlled by sedimentary hydrodynamic environment, while the content variation of Ba and Cd are controlled by human activities. And the contents variation of Pb and Zn are influenced by both natural source and human activities. ④ The average potential ecological risk index of heavy metals in surface sediments in the cooperation zone is 140.79, in generally serious state. This is mainly caused by Cd, indicating the monitoring of Cd should be strengthened. The research results could provide scientific basis for the sustainable development, environmental protection and governance of Guangdong-Macao in-depth cooperation zone in Hengqin.