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Nanostructuring photocatalytic and catalytic materials substantially increases the surface‐to‐volume ratio, thereby exposing a greater number of active sites essential for enhanced catalytic efficiency. However, optimizing these efficiencies requires the non‐destructive,operandointerrogation of individual nanocrystals under realistic catalytic conditions—a capability that has long remained elusive. Here, this challenge is addressed by reporting three‐dimensional imaging of defects, crystal morphology, and strain dynamics in individual Bi₂WO₆(BWO) nanoflakes using Bragg coherent diffractive imaging (BCDI) underoperandotemperature, gas, and light‐driven conditions. It is demonstrated that maintaining a constant temperature of 40°C thermally activates charge carriers, likely enhancing their mobility and reducing recombination rates. Furthermore, an Argon (Ar) gas flow stabilizes the reaction environment, while a mixed Hydrogen–Nitrogen (H₂+ N₂) flow induces a hydrogen‐triggered semiconducting‐to‐metallic (SM) electronic phase transition accompanied by a structural transformation, as supported by density functional theory (DFT) calculations. Both DFT and BCDI analyses reveal that during the SM phase transition, a new structural phase nucleates near defects and propagates inhomogeneously. Notably, the onset of nanoscale cracking is observed, driven by localized strain accumulation and environmental cycling, which increases surface area and potentially introduces new reactive sites. These findings illustrate that combining advanced nanostructuring withoperandoimaging techniques can provide critical insights into the local structural features that govern photocatalytic performance, paving the way for the rational design of next‐generation photocatalytic materials.