Objective To explore the application of peer education in TB prevention at middle schools in Kai County of Chongqing and compare it with traditional education, and to provide theory support for further policy making. Methods Four complete middle schools were randomly selected as the control group, the peer education group, the traditional education group and the combined group of peer education and traditional education, respectively. Effect evaluation was performed one month later (instant evaluation) and six months later (long-term evaluation), respectively, after the intervention period. Results The instant and long-term evaluation showed that the knowledge, attitude and practice scores of the three intervention groups were higher than the scores before intervention or those of the control group (Plt;0.01). Besides, the behavior score of the peer education group had no significant difference between instant and longterm evaluation. All scores in the instant evaluation were higher than those of long-term evaluation both in the peer education group and the traditional education group (Plt;0.01). For the knowledge, attitude and practice scores, there was no significant difference between instant and long-term evaluation in the combined group of peer education and traditional education. Conclusion Compared with the peer education group and the traditional education group, the combined group achieves an enduring effect. There is obvious instant effect in the traditional education group, and peer education has a long-term influence on students’ behavior.