Using data collected from two provinces in China through an online survey, the current study aimed to investigate left‐behind children's emotional and academic adjustment during the COVID‐19 pandemic in China. The participants included 1780 left‐behind (960 boys) and 1500 non‐left‐behind (811 boys) children in elementary and junior high school with a mean age of 11.23. Self‐reported questionnaires concerning children's depression, loneliness, anxiety, and academic adjustment, and parents' coping with children's negative emotions were completed. The results suggested that compared with non‐left‐behind children, left‐behind children's depression and anxiety symptoms were more severe and their academic adjustment was poorer. However, left‐behind children had lower levels of loneliness than non‐left‐behind children. Additionally, supportive coping types, especially emotion‐focused and problem‐focused reactions, were significantly negatively correlated with children's depression and anxiety. Unsupportive coping types, especially distress and punitive reactions, were significantly positively correlated with children's depression and anxiety symptoms. Moreover, the relationships between punitive reactions and depression, ignoring and loneliness and problem‐focused reactions and academic adjustment were significantly stronger in left‐behind children. Hence, during the pandemic, left‐behind children were still at a disadvantage even with their parents' company. However, parents' coping style towards left‐behind children's negative emotions played a significant role in their adjustment.