Metabolites of the Jinyu 88, Huanong 18, and Demeiya 9 maize varieties from the same origin were isolated and identified by GC-MS, and the specific metabolites and metabolic mechanisms of these three varieties of maize were preliminarily analysed and discussed. The metabolites were extracted with 80% methanol and derived with N,O-bis(trimethylsilyl)trifluoroacetamide. A total of 59 metabolites were identified. The specific metabolites of these three varieties of maize were identified. Four possible unknown-structure metabolites were hypothesized. The results showed that the specific metabolites of JY88 were only involved in fatty acid metabolism. The specific metabolites of HN18 were determined to be involved in fatty acid metabolism, glucose metabolism, and phytosterol metabolism. The specific metabolites of DM9 were observed to participate in glucose metabolism and fatty acid metabolism. The disease resistance of HN18 was higher than that of DM9, and its grain bulk density was higher than that of DM9. JY88 was determined to be significantly different from the other two varieties, and its appearance and disease resistance were worse than those of the other two varieties. The variety with the highest nutritional value was determined to be HN18, and the variety with the lowest nutritional value was JY88. This finding indicated that different maize varieties from the same origin had different metabolites and different metabolic mechanisms, which caused the three maize varieties to exhibit different characteristics and qualities.