Picric acid (PA) is an organic substance widely used in industry and military, which poses a great threat to the environment and security due to its unstable, toxic, and explosive properties. Trace detection of PA is also a challenging task because of its highly acidic and anionic character. In this work, silver nanoparticles (AgNPs)-decorated porous silicon photonic crystals (PS PCs) were controllably prepared as surface-enhanced Raman scattering (SERS) substrates using the immersion plating solution. PA and Rhodamine 6G dye (R6G) were used as the analyte to explore the detection performance. As compared with single layer porous silicon, the enhancement factor of PS PCs substrates is increased to 3.58 times at the concentration of 10−6 mol/L (R6G). This additional enhancement was greatly beneficial to the trace-amount-detection of target molecules. Under the optimized assay condition, the platform shows a distinguished sensitivity with the limit of detection of PA as low as 10−8 mol/L, the linear range from 10−4 to 10−7 mol/L, and a decent reproducibility with a relative standard deviation (RSD) of ca. 8%. These results show that the AgNPs-modified PS PCs substrates could also find further applications in biomedical and environmental sensing.