Surface-enhanced Raman scattering (SERS) greatly increases the detection sensitivity of Raman scattering. However, its real applications are often degraded due to the unrepeatable preparation of SERS substrates. Herein presented is a very facile and cost-effective method to reproducibly produce a novel type of SERS substrate, a monolayer photonic crystal (PC). With a building block of laboratory-prepared monodisperse SiO2 particles deposited with space-tunable silver nanobulges (SiO2@nAg), a PC substrate was first assembled at the air–water interface through needle tip flowing, then transferred onto a silicon slide by a pulling technique. The transferred monolayer PCs were characterized by SEM and AFM to have a hexagonal close-packed lattice. They could increase Raman scattering intensity by up to 2.2 × 107-fold, as tested with p-aminothiophenol. The relative standard deviations were all below 5% among different substrates or among different locations on the same substrate. The excellent reproducibility was ascribed to the highly ordered structure of PCs, while the very high sensitivity was attributed to the strong hotspot effect caused by the appropriately high density of nanobulges deposited on SiO2 particles and by a closed lattice. The PC substrates were validated to be applicable to the SERS assay of trace thiol pesticides. Thiram pesticide is an example determined in apple juice samples at a concentration 102-fold lower than the food safety standard of China. This method is extendable to the analysis of other Raman-active thiol chemicals in different samples, and the substrate preparation approach can be modified for the fabrication of more PC substrates from other metallic nanobulge-deposited particles rather than silica only.