Web-based peer assessment can develop students' cognitive schema, help students construct their knowledge, promote students' positive attitudes towards discussing and cooperating with peers, and increase students' skills to undertake lifelong learning by using the information technology. The assessment can be said to be an evaluation method based on profound learning theory. Moodle is a free course management system. It has the characteristics of ease of installation and use, and open source code. Teachers can take advantages of the strengths of the system to implement web-based peer assessment. First of all, this article analyzes the meaning, theoretical basis and research findings of web-based peer assessment. Next, it generally introduces the structure and design of the system. Finally, it discusses the set up and application of peer assessment function on the Moodle ”Workshop” module. It is expected that this article can not only improve teachers' understanding of web-based assessment and the system but also develop their ability of implementing web-based peer assessment by using the system.