Seven genotype soybean seeds with different protein content were using as the raw material for natto fermentation. The study was focus on the difference of the sensory quality and properties of mucilage on the surface of natto after fermented by Bacillus subtilis natto. Then the relationship between the quality of mucilage and the quality traits of soybean seeds was analyzed. The results showed that, the sensory score and stretch length of natto mucilage fermented from five different genotype soybean except green soybean YSG-10 and black soybean YSB-37 were significantly negatively correlated with seeds protein content respectively (r are 0.953, 0.946 respectively, P＜0.05). Green soybean seed YSG-10 has a relatively low protein content, relatively low sensory score and relatively long stretch length; black soybean seed YSB-37 has the highest protein content, the lowest sensory score and the shortest stretch length, and yellow seed coat with low protein content soybean YSY-102 is suitable for fresh natto while the high protein content soybean YSY-23 is suitable for processing into natto powder, which can provide a reference for the selection and breeding of natto soybean.