Control deployment at airway intersections has always been a core issue affecting the efficiency of air traffic control (ATC). Previous research has primarily focused on a small number of aircraft flights. As a result, a pre-conflict resolution method of large-scale cross-flight flow based on autonomous diversion in the trajectory-based operations (TBO) environment was proposed. Firstly, based on the horizontal safety interval between aircraft, the minimum longitudinal time interval that should be maintained when an aircraft crosses the intersection was converted; secondly, the concept of occupancy time window was proposed, and a conflict detection mechanism based on the occupancy time window was established. By integrating the principle of the shortest passage time for flight flows, a multi-objective decision-making model was established to achieve precise identification of conflicting aircraft and determine their priority for diversion. Finally, to address the issue of insufficient timeliness of traditional heuristic algorithms in flight flow movement, the feasible solution space was reduced by limiting the turning angles, and a search model for the diversion points was established to minimize the diversion time, thereby improving the solution speed and search accuracy. An example of a typical high-altitude sector in northeastern China was used to verify the effectiveness of the proposed method for actual cross-route operation. The simulation results indicate that the domino effect parameter (DEP) of the proposed conflict resolution method is 18.2% lower than that of the speed regulation resolution method. The total time consumption for speed regulation resolution is 7.6 times that of the proposed method. Therefore, the proposed method has a lesser impact on spatial stability and a higher resolution efficiency.