CD38 is a nicotinamide adenine dinucleotide (NAD)-metabolizing enzyme responsible for catalyzing the synthesis of Ca^2+ messengers. Its inhibitor plays an important role in probing the regulatory pathway and physiological function of CD38. For clearly understanding the effect of 2'-substitution of nicotinamide mononucleotide (NMN) analogues on CD38 NADase inhibitory activity, a new kind of NMN analogues with two substituents at C-2' was investigated. Molecular dynamics (MD) simulation and quantum chemical calculation were used to investigate the mechanism by which 2'-substitution affects the inhibitory activity. The results showed that two substituents at C-2' interfered the formation of covalent bond between C-1' of NMN analogues and CD38. The findings of this study will be helpful for comprehensively clarifying the structure-activity relationships of NMN- related CD38 NADase's inhibitor.