The invention discloses an unmanned pollutant tracing system and method. The unmanned pollutant tracing system comprises an unmanned pollutant tracing boat, a hand-held remote controller and a remote monitoring base station. The unmanned pollutant tracing boat is in communication with the remote monitoring base station through GPRS and is in communication with the hand-held remote controller in a radio frequency communication mode. By the adoption of an embedded microcomputer system, a pollutant concentration detection device, a position and pose sensor, a GPS module and the like, the function of searching for a fixed sewage draining exit of a polluted drainage basin is achieved, the speed for positioning a pollution source after stealing emission of a factory is improved, and labor and capital investment are saved. Fixed-point and fixed-depth sampling can be achieved through the embedded system as a core system in cooperation with a three-dimensional sampling device, polluted water sampling is facilitated, and follow-up water quality analysis departments have resources, and the basis is provided for government departments for punishing pollution discharge enterprises.