School lunch plays an important role in children's healthy growth. Previous investigations revealed many problems with school lunches, including unreasonable dietary structure and insufficient micronutrients. This study aimed to assess the dietary structure and nutritional quality of lunches in Nanjing primary and middle schools. A stratified cluster random sampling method was used to select 44 schools that supply lunch in 12 districts in Nanjing, with two primary and two middle schools in each district. Twenty-four primary and twenty middle schools were selected. The Mann-Whitney U test was used to explore the influencing factors. Findings revealed a serious shortage of milk and fruit in school lunches; supply of eggs, fish, shrimp, and shellfish was less than half of the recommended quantity; livestock and poultry supply exceeded the recommended level by over four times. Energy and nutrition intake were suboptimal. Provision of energy, carbohydrates, vitamins (A, B1, B2, and C), calcium, and iron in urban primary schools was significantly higher than that in non-urban primary schools. The same pattern of significantly higher nutrients was equally seen in urban middle schools compared with non-urban middle schools, indicating that food supply was affected by regional economies. Therefore, it is urgent to improve the quality of lunches, with a particular focus on those in non-urban areas.