The digital transformation of education will bring changes in the connotation and relationship of curriculum content, teaching activities and other elements, and online learning and mixed teaching will become the mainstream teaching methods. While online learning brings many advantages, there are also problems such as lack of interaction between teachers and students and lack of emotional communication, which leads to the decrease of learners' student engagement level, which in turn affects learners' cognitive processing process and ultimately affects learning effectiveness. Pedagogical agent with emotion cues in virtual learning environment provides a more intelligent means to solve this problem. Pedagogical agent is a virtual role similar to a teacher, which is used in online learning environment to meet different teaching objectives, and can provide cognitive and emotional support for learners. However, unreasonable emotional cues design will lead to extra cognitive load for learners, thus affecting their cognitive level. In view of this, this study designed an pedagogical agent with rich emotion cues for online learning, and explored the changes of student engagement level by using Pre-test and Post-test and Social Network Analysis. The results show that in online learning, the emotion cues of pedagogical agent can significantly enhance degree of student engagement, effectively increase their learning motivation, and significantly improve their collaborative interaction levels.