The present invention relates to a method for predicting the trajectory of an aircraft based on the 4D flight path operation. An air traffic control system comprises a data communication module, a monitoring data fusion module, an airborne terminal module and a control terminal module. The monitoring data fusion module is used for realizing the fusion of the monitoring data of an air traffic control radar and automatic-dependent surveillance data so as to provide the real-time flight path information to the control terminal module. The control terminal module comprises two sub-modules: namely a preflight conflict-free 4D flight path generation sub-module, and an in-flight short-term 4D flight path generation sub-module. The method for predicting the trajectory of the aircraft depends on the control terminal module to process the data of a flight plan. Meanwhile, a hidden Markova model is adopted to generate a 4D flight path. Therefore, the analysis on the potential traffic conflict of the airspace traffic condition is realized. The method can effectively improve the safety of air traffic.