Learning persistence is a critical element for successful online learning. The evidence provided by psychologists and educators has shown that students’ interaction (student-student (SS) interaction, student-instructor (SI) interaction, and student-content (SC) interaction) significantly affects their learning persistence, which is also related to their academic emotions. However, few studies explore the relations among students’ interaction, academic emotions and learning persistence in online learning environments. Furthermore, no research has focused on multi-dimensional students’ interaction and specific academic emotions. Based on person-environment interaction model and transactional distance theory, this study investigates the relationship between students’ interaction and learning persistence from the perspective of moderation and mediation of academic emotions including enjoyment, boredom, and anxiety. Data were collected from 339 students who had online learning experience in China. AMOS 22.0 (IBM, Armonk, NY, USA) and SPSS 22.0 (IBM, Armonk, NY, USA) were employed to analyze the mediating and moderating effects of academic emotions, respectively. The results revealed that students’ interaction and academic emotions directly related to learning persistence. Specifically, enjoyment, anxiety and boredom had significant mediating and moderating effects on the relationship between students’ interaction and learning persistence. Based on these findings, we further discussed the theoretical and practical implications on how to facilitate students’ learning persistence in online learning environments.