Photonic crystals (PhCs) possess outstanding optical properties that can be exploited for chemical sensing. We utilized a three-dimensional close-packed PhC structure made of functionalized silica nanoparticles. They consist of alternating high and low refractive index regions and have optical properties, such as photonic band structures, that are very sensitive to the change of physical structures. This study used 2,4,6-trinitrotoluene (TNT) to illustrate a detection method based on the transmissive photonic band edge shift (TPBES) due to the binding of TNT with amine anchored on particle surfaces to form Meisenheimer (amine-TNT) complexes. PhCs are exceptionally sensitive to a small change in refractive index caused by surface modification. As a result, they are suitable for sensing specific reactions between an amine and TNT. This method achieved a wide detection range of TNT concentrations from 10$\mathrm{<mrow\; data-mjx-texclass="ORD">-12</mrow>}$ to 10$\mathrm{<mrow\; data-mjx-texclass="ORD">-4</mrow>}$ M. 2,4-Dinitrotoluene (DNT) and toluene were used as a control and blank, respectively. Because of gravitational sedimentation, the TNT-functionalized particles were self-assembled in pure ethanol. They were measured by UV–visible transmission spectroscopy. A three-dimensional model to simulate the detection system was built using the particles’ center-to-center distance (a) and effective dielectric constant (ε) as a function of the TNT concentrations. Two sets of simulations were performed: the first set involved a parametric sweep of the center-to-center distance of TNT-functionalized crystals using ε = 2.015. The second set involved a parametric sweep of the dielectric constant with a = 263.1 nm. These perturbations yield a TPBES response that is in agreement with our experimental results.