Whole wheat flour is a food raw material rich in macronutrients, but its application in baking industry is limited due to the existence of a large amount of insoluble dietary fiber in bran. In order to make full use of this resource, we first screened twelve cellulase-producing strains, and then extracted soluble dietary fiber (SDF) from whole wheat flour after fermentation with 3 strains of Aspergillus sp. and 2 strains of Bacillus sp., respectively. The effects of different strains on nutritional characteristics, SDF yield, structure improvement, and antioxidant activity of whole wheat flour were compared. The results showed that fermentation of whole wheat significantly increased the yield of SDF, the content of nutritive active substances, and improved the physicochemical structure and antioxidant activity of SDF in vitro. Scanning electron microscopy (SEM), X-ray diffraction and liquidity characteristics show that the fermentation to make whole wheat SDF has more porous microstructure and crystallinity of lower molecular weight. Fourier transform infrared spectrum showed that there were differences in functional group types between soluble dietary fiber in control group (C-SDF) and soluble dietary fiber in the fermentation group (F-SDF). These changes together improved the hydration performance and antioxidant activity of whole wheat SDF, including water holding capacity, oil holding capacity, cholesterol adsorption, 1,1-diphenyl-2-picrylhydrazyl (DPPH), 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) and hydroxyl radical scavenging, and lipase activity inhibition. Bacillus sp. SH and Aspergillus oryzae Y21 are ideal strains for fermentation of improved whole wheat, which has the potential of antioxidant properties while improving nutritional properties and food quality.