We proposed a new comprehensive index, the food quality index (FQI), to effectively evaluate food quality. The food quality index is based on chemical and biological indicators of the Chinese food standards framework. We evaluated the limit value regulations for infant formula standards and then established a comprehensive index and grading standard. Finally, we applied the index to evaluate data obtained from the Shenyang Product Quality Supervision and Inspection Institute. The results showed that the quality of older infant and young children formula (OF) was good, and the infant formula (IF) was acceptable. The quality of OF was observably higher than that of IF, and they were significantly different with a confidence interval of 99% (P=0.009<0.01). The most influencing factor of the IF and OF was minerals, followed by major components, optional ingredients, vitamins, and Pathogenic bacteria had no effect. In IF, The number of the main influencing single indicators were 36 and 20 in IF and OF, respectively. Statistical analysis showed that index values of vitamins in the two kinds of milk powders were significantly different, with a confidence interval of 99% (P < 0.01). Optional ingredients were significantly correlated, with a confidence interval of 95% (P = 0.015 < 0.05).