Protein is the one of the most important material basis of life. Insufficient or excessive protein intake and unbalanced amino acid intake will have a great impact on health. The current food protein quality evaluation system is based on the bioavailability of protein and amino acids, without considering the health effects of amino acids. This paper reviewed the research progress of traditional protein quality evaluation system, pointing out the challenges faced by the traditional protein quality evaluation system. For the first time, a new index “methionine score (MS)” was introduced based on the traditional protein quality evaluation system, and the definition and calculation formula of MS were given, It is suggested that it should be combined with the digestible indispensable amino acid score (DIAAS) in the traditional protein evaluation system, and the health effects of amino acids should be considered while evaluating the utilization rate of amino acids, so as to supplement the traditional food protein quality evaluation system.