It generally is accepted that concept mapping has a noticeable impact on learning. But literatures show the use of concept mapping is not benefit all learners. The present study explored the effects of incorporating computer-based concept mapping in physics instruction. A total of 61 9th-grade students participated in this study. By using a quasi-experimental research approach, 31 students were assigned to a group that received computer-based concept mapping assisting instruction (CBCM), and 30 students were assigned to a constructive activities group that received "Work, Power, and Energy Curriculum" instruction without concept mapping assistance (NCM). Both groups participated for eight weeks, with four sessions per week and 45 minutes per session. A pre test-post test control group design was employed. The findings revealed that the CBCM group students scored higher than the NCM group students on the cognition understanding and higher order thinking subtests. No significant differences were found in the conception memorization subtest. In the retention test, the students in the CBCM group outperformed the students in the NCM group on all subtests. The results of the current study revealed that concept mapping activities effectively promote higher order thinking and knowledge retention.