Objective To find out the characteristics of amino acid composition and the differences of nutritional value of Coix lacryma-jobi in Fujian Province. Methods Taking Coix lacryma-jobi from Nanping, Putian, Sanming, Liaoyang, Guizhou and Yunnan as experimental materials, the amino acid content of Coix lacryma-jobi was determined by acid hydrolysis method and automatic amino acid analyzer. Based on the protein model recommended by Food and Agriculture Organization of the United Nations/World Health Organization (FAO/WHO) and the egg protein standard model, score of ratio coefficients of amino acids (SRC) of Coix lacryma-jobi was calculated and compared. At the same time, the changes of amino acids in Coix lacryma-jobi in different areas before and after storage for 10 months were studied, and the mechanism of amino acid changes in Coix lacryma-jobi during storage was discussed. Results There were 17 kinds of protein amino acids in Coix lacryma-jobi in 6 areas, with the total amino acids of 7.34-17.97 g/100 g. The amino acid content of Coix lacryma-jobi in Liaoyang area was the highest, followed by Putian area Coix lacryma-jobi, while Sanming area Coix lacryma-jobi exhibited the lowest levels. After 10 months of storage, the total amino acid content of Nanping area Coix lacryma-jobi remained relatively stable. In contrast, Coix lacryma-jobi from other regions showed varying degrees of decline in total amino acids. Notably, Sanming area Coix lacryma-jobi demonstrated a significant increase in the total amino acid content from 7.34 g/100 g to 11.17 g/100 g, representing a 52.2% rise. The total essential amino acids (TEAA) in Coix lacryma-jobi ranged from 1087 to 2389 mg/g N. The essential to total amino acid ratio (E/T, 33.82%-39.29%) and essential to non-essential amino acid ratio (E/N, 51.09%-64.71%) indicated that Liaoyang area Coix lacryma-jobi had the highest TEAA, whereas Sanming area Coix lacryma-jobi had the lowest, with both falling below the egg protein reference pattern. However, Putian and Liaoyang area Coix lacryma-jobi surpassed the FAO/WHO reference standards in terms of TEAA, E/T and E/N ratios. The SRC of Coix lacryma-jobi was 39.71-48.30 from 6 origins, and the highest score was Coix lacryma-jobi in Nanping area and the lowest was Coix lacryma-jobi in Liaoyang area. Lysine was the first restrictive amino acid, followed by methionine and cystine. Conclusion Coix lacryma-jobi contains a complete range of amino acids, giving it significant development and utilization potential. This can serve as a basis for evaluating the quality of Fujian Coix lacryma-jobi.