Objective: The long-term protective effect of self-compassion on mental health remained unclear in the pandemic context. This study aimed to investigate the trajectories of depression and anxiety symptoms and the role of self-compassion during the pandemic. Methods: In this one-year five-wave longitudinal study (retested every three months from February 2020 to February 2021), 494 Chinese college students completed the study through online questionnaires and provided information on depression and anxiety symptoms, self-compassion, and sociodemographic variables. Independent and joint trajectories of depression and anxiety symptoms were explored by growth mixture models. Predictive effects of self-compassion on trajectories were examined by logistic regression models. Results: Four and three heterogeneous latent trajectories were identified for depression and anxiety symptoms, respectively. Three distinct joint trajectories of depression and anxiety were determined: low symptoms group (54.0 %), mild symptoms group (34.4 %), and risk group (11.5 %). Participants with higher levels of self-compassion were more likely to follow the low symptoms trajectory of depression and anxiety symptoms (all p < 0.001). Conclusions: Group heterogeneity existed in the trajectories of depression and anxiety symptoms. Improving the levels of self-compassion would help to prevent and alleviate depression and anxiety symptoms. Programs based on self-compassion are encouraged to cope with the mental health challenges in the pandemic context.