To recycle and reuse food wastes, soybean curd residue (SCR) and wet corn distillers’ grain (WDG) were used as substrates in Bacillus subtilis fermentation to extract nattokinase (NK). The extract conditions of Natto-NK, as well as the fibrinolytic activity of SCR-NK, WDG-NK and Natto-NK were investigated. It was showed that the highest Natto-NK yield could reach 0.108 g per 150 g Natto (wet), when extract conditions were involved with saline (0.9%) 375 ml, (NH4)2SO4 30 g and the ratio of 3/4 between ethanol and saline. After fibrin hydrolysis for 4 h, both hydrolyzed areas of SCR-NK and WDG-NK were 49 mm2 in one hole, consistent with that of Natto-NK. Apart from this, as a result calculated according to the dried substrate, the SCR-NK yields (0.415 g/150 g) were significantly higher than Natto-NK yields (0.270 g/150 g). Moreover, SCR-NK (1.3 fibrinolytic unit/ml (FU/ml)) showed superior activity compared with that of Natto-NK, although there was no statistics difference. Our results suggested that SCR could be regarded as a promising fermentation source for NK production.