The popularity of instant messaging (IM) system creates a new way for human communication. Along with this trend, IM system is broadly applied in cooperative learning. There isn't much academic research forgetting this topic. In this research we examine how students use IM system during group discussion and analyze how IM system works through interviews and questionnaires. Based on the research results, we provide suggestions for IM system operation interface design in cooperative learning that makes the cooperative learning more efficient.