This paper presents the Semifree Flight theory used in a civil air traffic control (ATC) system to improve the capability of the traditional Free Flight mode. The progressiveness and hidden defects of the “Free Flight” model in civil aviation are analysed, and the Semifree Flight ATC system mode is introduced. Moreover, this paper presents the collaborative route planning method, which is the most important method used in the Semifree Flight ATC system. This collaborative route planning method can plan routes for each aircraft (either in flight or just before achieving flight) in real time, and the routes can satisfy all the safety constraints. The final numerical simulations verify the correctness and practicability of the Semifree Flight theory and the collaborative route planning method.