Two multilayer (ML) structures, composed of five layers of silicon-rich oxide (SRO) with different Si contents and a sixth layer of silicon-rich nitride (SRN), were deposited by low pressure chemical vapor deposition. These SRN/SRO MLs were thermally annealed at 1100 °C for 180 min in ambient N2 to induce the formation of Si nanostructures. For the first ML structure (MLA), the excess Si in each SRO layer was about 10.7 ± 0.6, 9.1 ± 0.4, 8.0 ± 0.2, 9.1 ± 0.3 and 9.7 ± 0.4 at.%, respectively. For the second ML structure (MLB), the excess Si was about 8.3 ± 0.2, 10.8 ± 0.4, 13.6 ± 1.2, 9.8 ± 0.4 and 8.7 ± 0.1 at.%, respectively. Si nanopyramids (Si-NPs) were formed in the SRO/Si substrate interface when the SRO layer with the highest excess silicon (10.7 at.%) was deposited next to the MLA substrate. The height, base and density of the Si-NPs was about 2–8 nm, 8–26 nm and ~6 × 1011 cm−2, respectively. In addition, Si nanocrystals (Si-ncs) with a mean size of between 3.95 ± 0.20 nm and 2.86 ± 0.81 nm were observed for the subsequent SRO layers. Meanwhile, Si-NPs were not observed when the excess Si in the SRO film next to the Si-substrate decreased to 8.3 ± 0.2 at.% (MLB), indicating that there existed a specific amount of excess Si for their formation. Si-ncs with mean size of 2.87 ± 0.73 nm and 3.72 ± 1.03 nm were observed for MLB, depending on the amount of excess Si in the SRO film. An enhanced photoluminescence (PL) emission (eight-fold more) was observed in MLA as compared to MLB due to the presence of the Si-NPs. Therefore, the influence of graded silicon content in SRN/SRO multilayer structures on the formation of Si-NPs and Si-ncs, and their relation to the PL emission, was analyzed.