Abstract: To study the relationship between agronomic trait groups yield and quality trait groups of grey speck immune soybean, Canonical correlation analysis in 17 soybean cultivars and the establishment of a comprehensive selection index for yield are reported in this paper. The result showed that: the most important factors for seed yield are yield group's seed per plant, 3- seed pod, pods per plant; agronomic trait group's growth period, knot per plant and plant height, agronomic character and yield group are positively correlated. Growth days and 100-seed weight are positively correlated, bottom pod height and 4- seed pod are negatively correlated; canonical correlation coefficient between agronomic character and quality group has reached the significant level; growth days and protein content are positively correlated, middle height plant, moderate grow period, more knots per plant, low pod position, middle seed, more seed per plant in yield character should be chose as breeding goal, protein content can be improved by selection of grow days and 100-seed weight character.