This study explores the relationship between adolescents’ perceptions of epidemic risk and their emotions through three follow-up surveys during the early stages of the COVID-19 pandemic on February 11th (T1), 18th (T2), and 25th (T3), 2020. Three hundred and four adolescents in different academic stages (junior high middle school, senior high middle school, and university) participated in the online survey, and cross-lag analysis was used to examine the causal relationship between epidemic risk perceptions and positive and negative emotions. The results found that the individual’s positive emotions were significantly higher than the negative emotions in T1, T2 and T3. Cross-lag analysis found that for positive emotions, T2 positive emotions could negatively predict T3 epidemic risk perceptions, and T2 epidemic risk perceptions could negatively predict the individual’s T3 positive emotions. For negative emotions, risk perceptions at T1 could positively predict negative emotions at T2, and at the same time, negative emotions at T1 could also positively predict epidemic risk perceptions at T2. This indicates that during the early stages of the COVID-19 pandemic, there was a causal relationship between the perceptions of epidemic risk and the emotions of adolescents, and this relationship had high stability among groups of different genders and academic stages.