The invention relates to the technical field of radar detection, in particular to multi-station lightning VHF (very high frequency) radiation source three-dimensional positioning method and system. The method includes: acquiring elevation of lighting arriving a single station through double antenna arrays vertically disposed at the single station, establishing an equation set by three or more single-station elevations, and calculating to obtain an occurrence three-dimensional spatial position of a flashing radiation source. The invention provides the lightning VHF radiation source three-dimensional positioning system based on the method. The system comprises at least three single stations and a data processing center. Each single station comprises a radiofrequency antenna array, a GPS (global positioning system) clock module, and a signal acquisition and processing module. Compared with the like prior arts, the method and system enable the detection range of the single station to be effectively enlarged, the antenna arrays and the data acquisition equipment to be simpler, and equipment cost and erection cost to be lower. The method and system are capable of detecting three-dimensional spatial evolution characteristics of lightning in large range, have the functions of early lightning warning, estimation on lightning danger area and fierce thunderstorm danger and the like, and provide effective information for lightning disaster prevention and severe convection weather warning.