L-lysine is an important amino acid in animals and humans and NADPH is a vital cofactor for maximizing the efficiency of L-lysine fermentation. Dihydrodipicolinate reductase (DHDPR), an NAD(P) H-dependent enzyme, shows a variance in nucleotide-cofactor affinity in bacteria. In this study, we rationally engineered Corynebacterium glutamicum DHDPR (CgDHDPR) to switch its nucleotide-cofactor specificity resulting in an increase in final titer (from 82.6 to 117.3 g L-1), carbon yield (from 0.35 to 0.44 g [g glucose](-1)) and productivity (from 2.07 to 2.93 g L-1 hr(-1)) of L-lysine in JL-6 Delta dapB:: Ec-dapB(C115G,G116C) in fed-batch fermentation. To do this, we comparatively analyzed the characteristics of CgDHDPR and Escherichia coli DHDPR (EcDHDPR), indicating that hetero-expression of NADH-dependent EcDHDPR increased L-lysine production. Subsequently, we rationally modified the conserved structure of cofactor-binding motif, and results indicated that introducing the mutation K11A or R13A in CgDHDPR and introducing the mutation R16A or R39A in EcDHDPR modifies the nucleotide-cofactor affinity of DHDPR. Lastly, the effects of these mutated DHDPRs on L-lysine production were investigated. The highest increase (26.2%) in L-lysine production was observed for JL-6 Delta dapB:: Ec-dapB(C115G,G116C), followed by JL-6 Cg-dapB(C37G,G38C) (21.4%) and JL-6 Delta dapB:: Ec-dapB(C46G,G47C) (15.2%). This is the first report of a rational modification of DHDPR that enhances the L-lysine production and yield through the modulation of nucleotide-cofactor specificity.