We intended to precisely evaluate the dietary quality of male and female medical college students using canteen data from the “Intelligent Ordering System” (IOS), combined with the supplemental food frequency questionnaire (SFFQ) and the Chinese Healthy Eating Index (CHEI) in Shanghai, China, to explore the potential factors influencing dietary quality. A total of 283 college students with the average age of 24.67 ± 3.21 years and Body Mass Index of 21.46 ± 3.49 kg/m2 in the medical school were enrolled in this study, and an online questionnaire investigation was conducted to collect the general information, lifestyle behavior, and SFFQ. The dietary data of the study participants from the school canteen were exported from the IOS of the Information Office of Fudan University. The CHEI consists of 17 components and the total score is 100, with a maximum score of each component of 5 or 10. We calculated each component score of the CHEI and aggregated the total score for male and female study participants. The Chi-square test and Wilcoxon rank sum test were employed in comparing the differences between the demographic characteristics and CHEI component scores of males and females. Univariate and multiple linear regression models were employed to examine the potential influencing factors of the total CHEI score. The CHEI median score was 66.65, and the component score for total grains was relatively low. Added sugars was the most overconsumed CHEI component. There were relatively serious deficiencies, based on the CHEI component scores, in fruits, soybeans, fish and seafood, and seeds and nuts in both sexes. Females had significantly higher CHEI scores than males (68.38 versus 64.31). The scores for tubers, total vegetables, dark vegetables, fruits, fish and seafood, dairy, and red meats were significantly higher in females than in males. Influencing factors including sex, education, dietary health literacy, and amount of time spent sedentarily were significantly associated with CHEI score. Our research revealed that the overall dietary quality needs to be further improved for college students at the medical school in Shanghai, China, with low intakes of total grains, fruits, soybeans, fish and seafood, and seeds and nuts, and high intakes of added sugars. Compared with males, females showed higher diet quality and conformed more strongly with the recommended Dietary Guideline for Chinese. Education, dietary health literacy, and amount of time spent sedentarily should be noted for improving the dietary quality of college students.