In this work, a new method of direct laser writing patterned photonic crystal heterostructure on a glass surface is proposed. A multi-heterostructure photonic crystal (MHPC) is predeposited on the glass surface and then the laser spot is focused on it and moves according to the set program, leading to the formation of patterned MHPC. Scanning electron microscopy (SEM) and finite element simulation show that the patterning is caused by the local thermal annealing of the polymer colloidal spheres through the thermal conduction effect of the substrate on the laser energy. The patterned area presents a function of the water confinement effect and can be used as a high-performance droplet analysis chip. By integrating the patterned MHPC array and seven fluorescent dyes, nine metal ions can be successfully recognized and discriminated. This approach is quite facile and fast for designing colloidal photonic crystals with controllable patterns. Moreover, it is of considerable significance for the practical application of photonic crystal heterostructure in the detection, sensing, anti-counterfeiting, and display fields.