Cucurbita species ( Cucurbita moschata and Cucurbita maxima) are rich sources of nutrients, especially carotenoids and carbohydrates. Metabolites in pulps of C. moschata and C. maxima lines were examined by high-performance liquid chromatography and gas chromatography–mass spectrometry. Our results revealed that glucose and sucrose were the dominant sugars in C. maxima and C. moschata, respectively. A correlation was found between Brix percentage and sucrose levels as compared with glucose and fructose. A greater amount of myo-inositol had accumulated in C. moschata lines compared with C. maxima. Conversely, total carotenoids and antioxidant activity were found to be higher in C. maxima lines than in C. moschata. A strong correlation of glucose, fructose, and sucrose with β-carotene and violaxanthin revealed that it will be difficult to develop pumpkin cultivars with both high inositol and carotenoid levels. In conclusion, the composition of carbohydrates and carotenoids was more diverse in C. moschata lines than in C. maxima lines. Our results will contribute to a better understanding of metabolite changes in the fruits of these as well as other pumpkin species.