In order to study the physicochemical and nutritional characteristics of kiwifruit varieties, 14 kiwifruits from different species with different flesh colors were selected for research. The pectin content was significantly higher in green-fleshed kiwifruits than those in red-fleshed and yellow-fleshed kiwifruits. Red-fleshed kiwifruits had the highest total flavonoid content, and green-fleshed kiwifruits in A. eriantha had the highest chlorophyll a content, chlorophyll b content and total carotenoid content. The energy and carbohydrate contents of yellow-fleshed kiwifruits were significantly lower than those of red-fleshed kiwifruit. Moreover, the protein contents in A. chinensis and A. chinensis var. deliciosa were higher than those in other species. The content of vitamin C in A. eriantha was far higher than in other kiwifruits. Red-fleshed kiwifruits had a significantly higher vitamin E and vitamin B1 content than green-fleshed kiwifruits. In addition, 1-pentanol, trans-2-hexen-1-ol, n-hexane and styrene presented only in red-fleshed kiwifruits. Therefore, these could be used as a characteristic fragrance for red-fleshed kiwifruits. Moreover, the varieties were ranked comprehensively by principal component analysis (PCA), among which the top four highest-ranking kiwifruits among the 14 varieties were ‘Huate’, ‘MHYX’, ‘Jinkui’ and ‘Xuxiang’, respectively. This study provides a reference for consumers and markets on quality improvement and processing.