Concerning of the low accurate rate of active defense technology, a heuristic detection system of Trojan based on the analysis of trajectory was proposed. Two kinds of typical Trojan trajectories were presented, and by using the behavioral data on Trojan trajectory the danger level of the suspicious file was detected with the decision rules and algorithm. The experimental results show that the performance of detecting unknown Trojan of this system is better than that of the traditional method, and some special Trojans can also be detected.