Longitudinal evidence demonstrating the association between parental absence and depressive symptoms in adolescence is limited. The present study aimed to explore this relationship in a Chinese national representative sample. This research was based on the China Family Panel Studies and included 1481 subjects. Depressive symptoms were assessed using the self-reported Center for Epidemiologic Studies Depression questionnaire. A multiple logistic regression model with a generalized estimating equation was used to test the association between parental absence and adolescent depressive symptoms. In the baseline year, 2012, 29.03% and 43.75% of adolescents had maternal and paternal absence, respectively. The prevalence of depressive symptoms increased from 23.23% to 28.12% in subsequent years. After controlling for covariates, maternal absence was positively associated with depressive symptoms (odds ratio 1.69, 95% confidence interval 1.06–2.68). Maternal absence led to depression in adolescents. It may be beneficial for adolescents with depression to spend more time with their mothers.