With increasing demand for public security and environmental protection, it is highly desirable to develop strategies to identify trace explosives (e. g., 2,4,6-trinitrotoluene (TNT)). Herein, we report novel photonic crystal (PC)based sensor chips for trace TNT detection by using amplification effect of PCs on fluorescence (FL) signals. The sensor chips are constructed by integrating silica nanoparticles (NPs) modified with (3-aminopropyl)triethoxysilane (APTES) and fluorescein isothiocyanate isomer (FITC) and PC substrates. The amino groups on FITC-APTES-silica NPs can specifically bind with TNT molecules to form Meisenheimer complexes and strongly quench the FL signal of neighboring fluorophores FITC through Förster resonance energy transfer. PCs with matched PBG can amplify the FL signal of FITC-APTES-silica NPs about 24.4-fold and significantly improve sensitivity and resolution of trace TNT detection with the limit of detection of 0.23 nM. The PC-based sensor chips are stable, sensitive, and reliable TNT sensing platforms, showing great potential in homeland safety and environmental protection.