Objective To study the difference of nutritional quality of different varieties of Prunus avium . Methods Taking 12 varieties of Prunus avium from Yantai of Shandong Province as the research object, the quality differences of different varieties of Prunus avium were analyzed by measuring the appearance indexes such as cross diameter and color difference, as well as the flavor and nutritional indexes such as soluble solids, organic acids, vitamin C, phenolic acids, flavonoids and anthocyanins. The one-way analysis of variance was used to clarify the differences in the content of each indicator among different varieties. The core quality indicators of Prunus avium were screened by correlation analysis, principal component analysis and cluster analysis. Results The soluble solids were found to be more than 15%, the titratable acid content was more than 0.5 g/100 g, and the purple-red fleshy cherry was rich in anthocyanins, and the determination of 26 quality indicators was simplified, 4 core indicators were determined to be chlorogenic acid, vitamin C, cyanidin-3-O-rutinoside, proanthocyanidins B₂. Based on the core indicators, Prunus avium could be completely separated by color, indicating that the core indicators were feasible. Finally, principal component analysis was used to comprehensively evaluate the quality of Prunus avium. According to the comprehensive score, it was found that the purple-red fleshy Russian cultivar had the best quality. The results of the measured quality index showed that it had the highest content of cyanidin-3-O-glucoside and rutin. Conclusion There are significant differences in the nutritional quality indexes of different varieties of Prunus avium. This paper provides data support for the construction of cherry quality indicator database, which is of great significance for standardizing the cherry quality evaluation system and promoting the high-quality development of the Prunus avium industry.