Insomnia, anxiety, and depression commonly co-occured and were closely related. Most of the prior studies were cross-sectional, with a poor ability to infer causality. Longitudinal study was needed to classify the relationships. The present study conducted a longitudinal study of non-clinical young Chinese males to investigate whether insomnia predicted the likelihood of future anxiety and depression, and vice versa. Convenient sampling method was applied, and 288 participants was recruited from Shanghai in October 2017 with Athens Insomnia Scale (AIS), Generalized Anxiety Disorder-7 (GAD-7) and Patient Health Questionnaire-9 (PHQ-9). 120 of them were re-tested in June 2018. The drop-out rate was 58.33%. Correlation analyses and cross-lagged analysis showed that AIS global score was significantly positively related with scores of depression and anxiety at baseline and follow-up. Insomnia was a predictive factor of anxiety, but it can’t predict depression. In sum, insomnia may be an important cause of anxiety, while no predictive relationship was found between insomnia and depression.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12888-023-04873-y.