Eight varieties of pepper seeds, namely Yuanzhu No.1, Yangjiao pepper, Xiangla595, Lafeng63, Lafenghong, Chentela, Xiangyan, Zhoupi pepper, were used as the studied materials, their soluble proteins and free amino acid compositions, contents and correlation were analyzed and the contents of flavor amino acid and taste active value were explored. The results showed that albumin contents were the highest in the eight varieties with 94.19-134.19 mg/g, and prolamin contents were the lowest(0.46-5.91 mg/g). Twenty four kinds of free amino acids were detected and the total contents were 12.22-27.51 mg/g, including 9 essential amino acids(3.94-6.32 mg/g), 2 semi-essential amino acids(1.13-2.71 mg/g) and 13 non-essential amino acids(7.15-19.52 mg/g). The contents of asparagine, aspartic acid, glutamine, threonine et al were maintained at higher level. The taste active value of flavor amino acids indicated that the main flavor amino acids in Yuanzhu No. 1, Xiangla595, Lafeng63, Lafenghong, Chentela and Zhoupi pepper seeds were sweet amino acid, but Yangjiao pepper and Xiangyan were umami amino acid. The cluster analysis of free amino acids showed that Zhoupi pepper was clustered with Chentela and Xiangyan, Lafenghong was clustered with Xiangyan595 and Lafeng63, and Yangjiao pepper was clustered with Yuanzhu No. 1. The correlation analysis showed that the contents of 9 groups of amino acids(arginine and methionine, citrulline and hydroxyproline and valine respectively, threonine, serine and glutamine in pairs, isoleucine, tyrosine and leucine in pairs) were positively correlated with each other, the contents of 23 groups of amino acids were positively correlated with each other, and the contents of 3 groups were negatively correlated with each other. The absolute value of the correlation coefficient between most amino acids contents were greater than 0.3, indicating that the correlation between each amino acid was strong.