Metal–halide perovskite nanocrystals (NCs) have gained significant attention in the field of optoelectronic and photonic devices due to their promising applications. Despite their exceptional optical properties, the impact of different synthetic strategies on the fundamental nature of NCs, such as nonradiative recombination centers, remains poorly understood. In this study, we investigated the photophysical properties of CsPbBr₃ NCs synthesized using two distinct methods, hot injection and ligand-assisted reprecipitation, at the individual particle level. We observed different blinking behaviors under specific photoexcitation power densities and proposed, through intensity–lifetime analysis and Monte–Carlo simulations, that these different synthetic strategies can fabricate NCs with similar crystal structures but distinct surface quenchers with varying energy levels, which significantly affected the photo-induced blinking-down and blinking-up behaviors in individual NCs. Our findings indicate a practical and feasible approach for controlling defect engineering in perovskite NCs, with significant implications for their use in optoelectronic and other technological applications.