The problems of campus violence such as acquaintanceship in Internet, suicide and sexual harassment occur very often. Related research results showed that infusing the Gender Relationship and Communication into the web-based learning is urgent need for high school and vocational high school students. This study uses ”the e-learning web-side of problem-based Gender Relationship and Communication” and ”involving problem-based Gender Relationship and Communication e-learning teaching materials” to instruct students. The purpose of this study was to explore the learning effect and investigate the influenced problems. A quasi-experimental design was utilized and purposive sampling was conducted at a high school and a vocational high school in Taiwan. One hundred thirty three eleven grade students were assigned into experimental and control group in each school. In this study, quantitative and qualitative research methods were used, and they included Survey, Observation records analyzing and focus group. The findings of this study including: (1) Using problem-based Gender Relationship and Communication e-learning can promote the learning effectiveness of experimental and control groups significantly in both of the school. (2) The problem-based learning effect of face to face learning is significant than e-learning learning in high school. (3) The problem-based learning effect of e-learning learning is significant than face to face learning in vocational high school. (4) The students suggest that diversity topics for discussion, multi-media materials, online psychological test and individual guiding may promote the learning effectiveness.