Web-based learning environments have not always enabled social interaction and equal participation of students. To solve this problem, the cooperative skills training was implemented in this study. The purpose of this study was to investigate the effect of cooperative skill training by different learning ability on Web-based cooperative learning. Subjects of this study were 70students sampled from first graders of high schools in Busan. It took 4 weeks for Web-based learning of science problem solving, the experiment groups was trained in Web-based cooperative skills for 2 weeks before Web-based learning. To examine the effect of cooperative skill training we analyzed the Web-based learning participation frequence in Web-based discussion and the scores on students\' problem solutions by different learning ability. The results from this study is as follows; First, Web-based cooperative group without cooperative skill training leads to the negative result such as rich-get-richer effect. Cooperative skill training of Web-based cooperative learning have an effect on the equal learning participation irrespective of the learning ability. Second, problem solving ability of middle and low learning ability students with cooperative skill training is higher than that of students without cooperative skill training. Therefore, this study suggests that cooperative skill training is of great importance for diminishing the rich-get-richer effect and free-rider effect, and increasing the students\' interaction in Web-based cooperative learning.