Rapid quantitative testing of illegal drugs is urgently needed for precisely cracking down on drug crimes. Herein, an optimized paper-based surface-enhanced Raman spectroscopy (SERS) platform with patterned printing of plasmonic nanoparticles was constructed for the on-site quick testing of illegal drugs in urine. The filter paper was first coated with a layer of positive-charged chitosan, so as to reduce its roughness by filling the holes of the cellulose matrix and enhance the adhesion of negative-charged silver ink. Subsequently, hydrophobic modification was performed based on the binary silylation reaction, which could obviously improve the sensitivity of the paper-based SERS substrate by concentrating the amount of analyte. Meanwhile, SERS-active silver ink was fabricated and further printed on the surface of the above modified paper with custom-designed pattern (3 × 6). The performance of this SERS platform was assessed by using crystal violet (CV) as a model tag, and the obtained results proved it possesses excellent sensitivity and reproducibility, in which the relative standard deviation (RSD) dropped remarkably. More importantly, as a proof of concept, rapid detection of standard methylamphetamine (MAMP), one of the most widely abused drugs, was achieved with a limit of detection (LOD) of 1.43 ppb using a portable Raman spectrometer. And it also had a good capability in human urine sample detection, with a correlation index (R2) up to 0.9927. This optimized paper-based SERS platform was easily manufactured, cheap, and portable, providing a new strategy for the on-site detection of illicit drugs.