Studies have shown that the prevalence of mental health problems is high among left-behind children (LBC). Modifiable eating habits may play an important role in promoting mental health among these adolescents. This study aimed to investigate the situation of dietary habits and their association with mental health problems in a sample of Chinese LBC. We conducted this cross-sectional study in an economically disadvantaged area of China in May 2020. Information on socio-demographic factors, eating habits (the frequency of eating carbohydrates, fruits, vegetables, protein, and breakfast), and mental health problems (insomnia, depression, and anxiety) were collected among local adolescents. Among 8939 adolescents were recruited, a total of 3314 LBC (1455 males and 1859 females, aged 12–17 years) were identified and included in the current study. Associations between dietary habits and mental health were analyzed by generalized linear models. Results indicated that the dietary pattern was unhealthy among LBC and even worse in females. Compared to routinely eating breakfast and fruits, lower frequencies of eating breakfast and fruits were identified as two significant factors with higher risks of mental health problems. Moreover, the association was more pronounced in females. Therefore, improving diet quality, particularly the frequency of eating breakfast and fruit intake may be an effective approach in the mental health promotion for LBC, especially for females.