The invention discloses a multi-machine multi-station joint three-dimensional task system and method. The system comprises a control terminal, a communication system, intelligent stations and a multi-machine platform; a plurality of intelligent stations are provided and arranged in different areas of a flight route and provide self-test, flight continuing, positioning and battery replacement services for flight bodies; the multi-machine platform receives the control instruction of the control terminal, performs analysis and data conversion, transmits obtained data to corresponding flight bodies, obtains the waypoint information and observation data of the corresponding flight bodies and transmits the waypoint information and observation data to the control terminal for storing the waypoint information and observation data; the communication system provides communication channels for the interaction of the multi-machine platform and the control terminals and the interaction of the intelligent stations and the control terminal; and the control terminal receives the control information of the multi-machine platform and the start and stop conditions of the flight bodies of the intelligent stations, receives the target data, environment models and state parameters of the flight bodies and adjusts the positions and attitudes of the flight bodies according to the received control information. With the multi-machine multi-station joint three-dimensional task system and method of the invention adopted, the autonomous flight continuing and long-term operation capacity of an unmanned aerial unit can be improved.