Hydrodeoxygenation (HDO) is a promising way to produce the second generation biodiesel from aliphatic acid based biomass. In this study, NixMoy@NC bimetallic catalysts with varying molar ratios were prepared using ZIF-8 as a representative MOF precursor. Lauric acid was chosen as the model compound, the catalytic performance of these catalysts with different metal ratios, reaction temperatures, and pressures was investigated. In addition, the reaction of lauric acid, lauric alcohol, and lauric aldehyde at different reaction times were investigated to explore the pathways of lauric acid. The influence of Mo doping on the catalyst structure, reducibility, and electronic properties was investigated through a series of characterizations, including SEM, TEM, XPS, H2-TPR, and NH3-TPD. This study revealed that the ZIF-8 support with incorporated Ni and Mo maintained a stable structure. Compared to Ni-based catalysts, the addition of Mo in the bimetallic catalyst can bring the electron transfer between Ni and Mo and increased the active sites and acid sites. An appropriate amount of Mo can lower the reduction temperature and enhance the catalytic activity for hydrogenation and deoxygenation reactions. Based on the catalytic experimental results, it can be observed that liquid alkanes, such as undecane and dodecane, are primarily formed through decarbonylation of lauric aldehyde and hydrodeoxygenation of lauric alcohol. Additionally, under high-temperature conditions, the hydrodeoxygenation reaction is favored over the decarbonylation reaction, promoting the production of dodecane. This indicates that Mo exhibits better activation for the C–OH reaction, leading to these observations. Under repeated use, the catalyst still has good catalytic activity and stability.