A paucity of public service afforded to migrant workers often begets a wide range of social problems. In China, hundreds of millions of migrant worker parents have to leave children behind in their hometowns. This paper investigated the long-term effects of the childhood experience of being left behind on the mental well-being of late adolescents. Mandatory university personality inventory (UPI) surveys (involving psychosomatic problems such as anxiety, depression, and stress) were conducted at a university in Jiangsu, China, during 2014–2017. The study sample consisted of 15,804 first-year college students aged between 15 and 28 years. The PSM method and the OLS regression model were employed. Controlling for the confounding factors (gender, age, single-child status, hometown location, ethnicity, and economic status), our empirical investigation demonstrated that childhood left-behind experience significantly worsened the mental health of the study sample, increasing the measure of mental ill-being by 0.661 standard deviations (p < 0.01). Moreover, the effects were consistently significant in subsamples divided by gender, single-child status, and hometown location; and the effects were greater for females, single-child students, and urban residents.