Direct visualization of spatiotemporal evolution of molecules and active sites during chemical transformation in individual catalyst crystal will accelerate the intuitive understanding of heterogeneous catalysis. So far, widespread imaging techniques can only provide limited information either with large probe molecules or in model catalyst of large size, which are beyond the interests of industrial catalysis. Herein, we demonstrate a feasible deep data approach via synergy of multiscale reaction-diffusion simulation and super-resolution structured illumination microscopy to illustrate the dynamical evolution of spatiotemporal distributions of gas molecules, carbonaceous species and acid sites in SAPO-34 zeolite crystals of several micrometers that are typically used in industrial methanol-to-olefins process. The profound insights into the inadequate utilization of activated acid sites and rapid deactivation are unveiled. The notable elucidation of molecular reaction-diffusion process at the scale of single catalyst crystal via this approach opens an interesting method for mechanism study in materials synthesis and catalysis.