Selective surface-enhanced Raman scattering (SERS) detection of target explosives with good reproducibility is very important for monitoring soldiers' health and ecological environment. Here, the specific charge transfer pathway was constructed between a stable nanodiamond-multilayer graphene (MGD) film substrate and the target explosives. Two-step wet chemical oxidation methods of H2O2 (30%) and HNO3 (65%) solutions were used to regulate the terminal structure of MGD films. The experimental results showed that the hydroxyl (-OH) functional groups are successfully modified on the surface of MGD thin films, and the MGD-OH substrates having good selectivity for 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) explosive in mixed solutions of the TATB, 2,2-dinitroethene-1,1-diamine, 2,4,6-trinitrotoluene, and 1,3,5-trinitroperhydro-1,3,5-triazine explosives compared with MGD substrates were demonstrated. Finally, first-principles density functional theory simulations revealed that the SERS enhancement of the MGD-OH substrate is mainly attributed to the transferred electrons between the -NO2 groups of TATB and the -OH groups of the MGD-OH substrate.