The conflict detection algorithm based on the three dimensional coordinate system was proposed to treat the flight conflict problems arisen from the development of Air Traffic Control in China. First of all, based on the features of the flight path, the conflict probability was solved after time integrating flight path and the efficiency of continuous solving conflict probability was improved. Then the flight conflict of the change of flight level during free flight in the three dimensional coordinate system was took into consideration. Plenty of experiment was simulated by using the method of Monte Carlo. The feature of track error and precision parameter was analyzed, which shows the effects of the track error and precision parameter on conflict probability and false alarm. The experiment result proved the availability and practicability.