Spectroscopic evidence of directed excitonic energy transfer (ET) is presented through size-gradient CdSe/ZnS nanocrystal quantum dot (NQD) layers into an underlying Si substrate. NQD monolayers are chemically grafted on hydrogen-terminated Si surfaces via a self-assembled monolayer of amine modified carboxy-alkyl chains. Subsequent NQD monolayers are linked with short alkyldiamines. The linking approach enables accurate positioning and enhanced passivation of the layers. Two different sizes of NQDs (energy donors emitting at 545 nm, and energy acceptors emitting at 585 nm) are used in comparing different monolayer and bilayer samples grafted on SiO2 and oxide-free Si surfaces via time-resolved photoluminescence measurements. The overall efficiency of ET from the top-layer donor NQDs into Si is estimated to approach ≈90% through a combination of different energy relaxation pathways. These include sequential ET through the intermediate acceptor layer realized mainly via the non-radiative mechanism and direct ET into the Si substrate realized by means of the radiative coupling. The experimental observations are quantitatively rationalized by the theoretical modeling without introducing any extraneous energy scavenging processes. This indicates that the linker-assisted fabrication enables the construction of defect-free, bandgap-gradient multilayer NQD/Si hybrid structures suitable for thin-film photovoltaic applications.