The purpose of this study was to explore the teaching effects of physiology by concept mapping in developing critical thinking ability and self-directed learning. Study was designed with a sample being drawn from a group in first-year junior college nursing students. Students in the experimental group were taught to use concept mapping in their physiology lectures. And students in the control group were taught by means of traditional methods. The long-term study was conducted for 18 weeks. And the short-term study was conducted for 9 weeks first, and then the concept mapping intervention was changed between control and experimental groups. After that the students got on another 9 weeks training courses. Both parts of the studies had shown consistently better overall self-directed learning than before. In particular the performance of effective learning was increased significantly in both control and experimental groups. However, the critical thinking ability was shown statistically significantly lower in experimental group than in control group in the long-term study. But this interference was not shown in the short-term study. The present study revealed that concept mapping is an effective tool to improve students' self-directed learning. However, the interference in critical thinking ability was found in the long-term study, which suggest that the elevation of critical thinking needs more than concept mapping intervention. Other teaching skills and tools should be involved in physiology teaching.