Previous studies have shown that negative automatic thoughts are important predictors of suicidal ideation. However, few studies have explored the underlying mechanisms of the association. The current study aimed to explore the potential mechanisms underlying the relationship between negative automatic thoughts and suicidal ideation by a longitudinal serial mediation model. A total of 1133 Chinese adolescents (51.2% males, Mage = 14.76 years, SD = 0.65) completed self-report questionnaires regarding negative automatic thoughts, self-disgust, depressive symptoms, and suicidal ideation. The assessment was conducted in three waves, 6 months apart. Descriptive statistical analysis showed that the 6-month prevalence of suicidal ideation was 33.4% for Wave 1, 32.5% for Wave 2, and 27.2% for Wave 3. Pearson correlation analysis showed that negative automatic thoughts, self-disgust, and depressive symptoms were all positively related to suicidal ideation. Regression-based mediation modeling showed that self-disgust and depressive symptoms were serial mediators of the relationship between negative automatic thoughts and suicidal ideation, with negative automatic thoughts influencing suicide ideation through three mediation pathways. The current findings suggest that self-disgust and depressive symptoms are potential mediating mechanisms that explain the link between negative automatic thoughts and suicidal ideation. Interventions that target negative automatic thoughts may be an effective way to reduce the risk of suicidal ideation. In addition, the important role of self-disgust in the development of depressive symptoms as well as suicidal ideation needs to be taken into account in therapeutic practice.