Volatile organic compound (VOC) pollution in surface water can affect the growth of microorganisms and even cause damage to human health. Quickly obtaining VOC distribution and tracing emission sources are of great significance to ensure the security of water quality. In this study, we developed a mobile shipborne spray inlet proton transfer reaction mass spectrometry (S-SI-PTR-MS) instrument for rapid and on-line detection of volatile organic compounds (VOCs) in surface water. It mainly consists of a shipborne platform, a spray inlet system, a proton transfer reaction mass spectrometer, and geographic information software (GIS). During the navigation, VOCs in water can be quickly extracted to gaseous state by the SI system and transferred into the proton transfer reaction mass spectrometry (PTR-MS) for detection. The GIS can receive VOC and longitude-latitude data at the same time. And then the identification and concentration information can be shown on an electronic map in real time. The limit of detection and response time were 1.32 μg/L∼9.43 μg/L and 56 s–114 s, respectively. The spatial resolution is 0.14 m in a common navigation experiment (5 km/h, dwell time = 0.1 s), allowing for high-resolution monitoring of VOCs in water. Finally, field experiments were performed on the lower Nanfeihe River and some surfaces of Chaohu Lake in China. During tracing pollution in Nanfeihe River, two VOC emission sources in the downstream were located, nearing a sewage outlet and a wharf, respectively. During imaging VOC distribution in the Chaohu Lake, we found the areas with high-concentration VOCs were mainly along the ship channel. The newly developed S-SI-PTR-MS can monitor water quality in surface water in real time and has the potential to assist environmental protection enforcement.