To identify the phenotypes and to classify the genotypes through genetic diversity, factors and cluster analysis, the content of protein and 16 amino acids was measured in 240 north soybean core collections. The results showed that there are higher genetic variation and diversity for the content of protein and 16 amino acids in 240 north soybean core collections. Three common factors were screened for clustering analysis according to the factor analysis. Seven genetic groups were divided through clustering analysis for 240 north soybean core collections. The sequence for protein content from high to low acted as group 7 > group 6 > group 5 > groups 2> groups 1> groups 3 > group 4. Change trend of 12 amino acids composition was in accordance with protein content. Group 7 and 6 for high protein genetic groups would be used as parent materials for gene polymerization breeding. 24 high methionine germplasm resources were identified by analysis, including Gongye 04L-141, Longpin 03-311, Proto, Helongyoutai, Maoyandou, Chasedou, Zihua 2, Dongnong 48. These germplasm resources are the material basis for innovation of high methionine germplasm.