Rapid industrialization and urbanization in China have resulted in labor migrants leaving children behind. For left-behind children (LBC), disrupted parental attachment may increase the risk of psychiatric morbidity in adulthood. To investigate psychopathological consequences for university students who were LBC and to estimate the effects of one or both parents being migrants, the duration of left-behind experience, and parental absence during critical periods of growth on psychiatric morbidity. We conducted an annual survey of all freshmen at a Chinese university from 2014 to 2018. The questionnaire collected information on left-behind experiences and psychiatric morbidity using standardized self-report instruments. Regression coefficients derived from logistic regression were used to measure the associations among total time left behind, absence of one parent or both parents, age when left behind and psychopathological consequences. A total of 42,505 students were included. Students who were LBC had more psychopathology, including depression, anxiety, somatoform disorder, obsessive–compulsive disorder, self-reported suicide attempts and deliberate self-harm, than those who were not. Students for whom one or both parents were migrants showed a greater risk of psychiatric morbidity. The risk of psychiatric morbidity increased with the length of parental absence. Left-behind experience during childhood represents sustained impacts for university students into early adulthood. The higher prevalence of psychiatric morbidity in young adults who experienced the absence of one or both of their parents, especially in their early childhood, suggests that other factors besides attachment, such as protection from other risks, are important and that further research is necessary.