Hazardous volatile organic compounds (VOCs) are one of the critical concerns in environmental water due to their toxicity to aquatic organisms and drinking water. Therefore, rapid detection of hazardous VOCs in environmental water is highly needed as many analytical methods are limited to on-site monitoring. In this work, we designed a novel unmanned shipborne mass spectrometer (US-MS) system for the real-time and online monitoring of hazardous VOCs in environmental water. The US-MS system consists of a miniaturized mass spectrometer, an automatic sampling device, a robust unmanned ship, and other monitoring and control devices. Along with the navigation route of the US-MS system, environmental water was continuously introduced into the MS system for the online and real-time detection of hazardous VOCs via a liquid/gas exchange membrane. Analytical performances of the US-MS system were investigated by a mixture of 10 VOCs showing low limits of detection (LODs: 0.31-1.26 ng/mL), good reproducibility (RSDs: 2.93-11.03%, n = 7), and excellent quantitative ability (R2 > 0.99). Furthermore, on-site detection and online monitoring of hazardous volatile contaminants such as benzene, chloroprene, and toluene in different aquatic environments such as rivers and lakes were successfully demonstrated, showing excellent field applicability of the US-MS system. Overall, the newly developed US-MS system could perform on-site, online, and real-time monitoring of complex VOCs in environmental water, showing good performances and versatile applications in water analysis.