The scarcity, richness, and other important physiological functions of D-psicose make it crucial to increase the yield of D-psicose. The production of D-psicose can be accomplished by D-psicose 3-epimerase (DPEase) from Clostridium bolteae (CbDPEase) catalyzing the substrate D-fructose. Although the catalytic efficiency of the CbDPEase has been raised via using the site-directed mutagenesis (Y68I/G109P) technique, structure-activity relationship in the wild-type CbDPEase and Y68I/G109P mutant is currently poorly understood. In our study, a battery of molecular modeling methods [homology modeling, adaptive steered molecular dynamics (ASMD) simulations, and Molecular Mechanics/Generalized Born Surface Area (MM-GB/SA)], combined with protein structure networks, were employed to theoretically characterize the reasons for the differences in the abilities of the D-fructose catalyzed by the wild-type CbDPEase and Y68I/G109P mutant. Protein structure networks demonstrated that site-directed mutagenesis enhanced the connectivity between D-fructose and CbDPEase, leading to the increased catalytic efficiency mediated by the functional residues with high betweenness. During the dissociation of the D-fructose from the Y68I/G109P mutant, planes of benzene rings of F248 and W114 could be continuously parallel to the stretching direction of D-fructose. It made the tunnel have an open state and resulted in the stable donor-π interactions between D-fructose and the benzene rings around 18Å. The stronger substrate-protein interactions were detected in the Y68I/G109P mutant, instead of in the wild-type CbDPEase, which were consistent with the binding free energy and Potential Mean of Force (PMF) results. The theoretical results illustrated the reasons that Y68I/G109P mutations increased the catalytic efficiency of CbDPEase and could be provided the new clue for further DPEase engineering.