The invention relates to a thunder positioning system and method. The system comprises a detection device, a data acquisition module and a data processing module; the detection device is cooperated and connected with the data acquisition module; the data acquisition module is cooperated and connected with the data processing module; and the detection device uses a nineteen-element cross-array microphone array. The microphone array uses a three dimensional cross type three-dimensional array structure which is composed of a cross type horizontal coordinate axis and a line type vertical coordinate axis. The method includes the following steps: thunder and lightning electromagnetic signals detected by the microphone array are sent to the data acquisition module, are pre-processed by the data acquisition module, and then are outputted to the data processing module; the data processing module uses a frequency domain beam forming algorithm to process step by step thunder signals obtained by the microphone on the horizontal coordinate axis and vertical coordinate axis; an azimuth angle and pitch angle of the thunder signal are determined; based on an arrival time difference between thunder and lightning, a distance of a thunder sound source is determined; and one single detection device can realize obtaining an accurate lightning location and a channel three-dimensional positioning result.