The invention relates to a method and a system for comprehensively and synchronously observing lightning stroke discharge. The method is based on a global positioning system (GPS) timing technology, and the lightning stroke discharge is observed by the observation system. The method comprises the following steps of: providing the activity trend of lightning storm by using a wide area lightning location system, and reminding the arrival of the lightning storm by using an atmospheric average electric field instrument; and outputting an alternating current (AC) B code signal to a high-speed image pickup device by using a GPS timing device, marking the formation time of each frame of picture by using a clock system, receiving a time to live (TTL) level signal from a lightning high-speed trigger device, outputting correct time t corresponding to a TTL level rising edge to a personal computer (PC), and recording the TTL level signal and electrical and acoustic measurement signals by using a high-speed data storage recorder. The system comprises the wide area lightning location system, a data analysis and processing server, the atmospheric average electric field instrument, the high-speed image pickup device, the lightning high-speed trigger device, a quick electric field change instrument, a slow electric field change instrument, a magnetic field measuring instrument, an array thunder detection device, the high-speed data storage recorder and the GPS timing device.