Objective: To analyze the nutritional literacy and influencing factors among students from Nutrition Improvement Program for Rural Compulsory Education Students (NIPRCES) in Chongqing, and to provide a scientific basis for improving the nutritional literacy of middle school students in the NIPRCES. Methods: Using cross sectional survey, a total of 3 365 students in the grade 7 and 8 were selected from the middle schools in 12 national pilot districts and 2 Chongqing pilot districts by online survey in September 2020. Students filled out a self designed nutritional literacy questionnaire anonymously. The relative evaluation method was used to convert the nutritional literacy of scores into a percentile, and the median score was used as the criterion for qualified nutritional literacy screening. Results: The median score of nutritional literacy of participants was 63.5, and 64.2% achieved the qualified level. The results of multivariate Logistic regression analysis showed that boarding school ( OR =1.28, 95% CI =1.08- 1.51 ) and no parents as the primary caregiver ( OR =1.22，95% CI =1.05-1.42) were associated with poor nutritional literacy. Urban residence ( OR =0.75, 95% CI =0.63-0.90), NIPRCES local pilot ( OR =0.83, 95% CI =0.71-0.97) and high paternal education ( OR =0.70, 95% CI =0.52-0.95) were associated with higher nutritional literacy ( P <0.01). Classroom was the main channel for students to obtain nutrition information at present (65.1%) and in the future (72.8%). Conclusion The nutritional literacy among students in the NIPRCES in Chongqing needs to be improved. Nutritional literacy level of students can be strengthened by nutritional education in boarding schools, rural areas, national pilot areas, and primary caregivers.