The invention relates to an air traffic control method based on 4D flight path operation. The method is implemented through an air traffic control system, and the air traffic control system comprises a data communication module, a monitoring data fusion module, an airborne terminal module and a control terminal module, wherein the monitoring data fusion module is used for fusing air control radar monitoring data with automatic related monitoring data and providing real-time flight path information for the control terminal module; the control terminal module comprises a preflight conflict-free 4D flight path generation submodule, a flight medium and short term 4D flight path generation submodule, a real-time flight conflict monitoring and alarming submodule and a flight conflict resolution 4D flight path optimization submodule. According to the air traffic control method based on 4D flight path operation of the system, the control terminal module is used for processing flight plan data and generating 4D flight paths through a hidden Markov model to analyze potential traffic conflicts of airspace traffic conditions, and a model prediction control theoretical method is adopted to provide the optimal resolution scheme. The method can effectively prevent flight conflicts and improve air traffic safety.