Biological dissociated soybean hydrolysates, which was yield in such of the enzymeassisted aqueous extraction of soybean oil processing, was used as research object, and applied for spray and microwave drying of peptiderich soybean protein meal powder, which was prepared under different conditions. The protein subunits of soybean meal composition, the rules of spatial conformation change of the protein phase volume, and the physical and functional properties of the peptide-rich soybean meal powder were in-depth investigated based on high performance liquid exclusion chromatography technology. Research results showed that the impact of spraymicrowave drying conditions on the HPLC-SEC peak intensity was significant, and 18~44ku proteins took 73.47%~89.36% of the total protein of the powder. The main component of soybean protein was globulin subunit, which was perhaps determined by the phase conversion rate, molecular collision between different proteins, aggregation opportunities and fibrosis at different spray speeds and microwave drying conditions, molecular weight of the enzyme dissociated soybean peptide-rich powder were also influenced under various conditions. In addition, the water solubility and dispersibility of biodissociated peptide-rich soy flour had similar trends under different microwave drying conditions, and reflected the same problem, which were related to the residual water content of the powder, the intensity of protein molecule movement, conformational changes, and aggregation and dissociation.