Small-molecule microarrays are powerful, high-throughput tools for gathering information about direct binding events between proteins of interest and small molecules. However, nonspecific binding on modified glass slides is the major factor reducing the quality of information obtained in proteomic screening with small-molecule microarrays. To improve the signal-to-noise ratio by suppressing the background signal, we tested several surface modification methods for glass slides. Jeffamine-coated slides showed a high fluorescence signal and a significantly enhanced signal-to-noise ratio. We applied this surface modification to proteomic screening of potential tyrosinase inhibitors with a small-molecule microarray and identified 2,4,4′-trihydroxychalcone as a new small-molecule binder to tyrosinase. Its actual binding and inhibitory effects on tyrosinase were validated using an SPR binding assay and an enzyme-based inhibition assay, respectively. Thus, we successfully demonstrate the application of Jeffamine-based modification to proteomics screening with small-molecule microarrays.