Controlled fabrication of semiconductor nanostructures with unique physicochemical properties is vital for future technologies. In this study, transformation from red‐emitting metal halide perovskite CH3NH3PbI3 nanocrystals (NCs) to green‐emitting CH3NH3PbBr3 NCs was achieved without significant morphological changes and loss of photoluminescence (PL) efficiency via a controlled halide exchange reaction. In situ single‐particle PL imaging along with detailed structural and elemental characterizations revealed that sudden cooperative transitions between two light‐emitting states via intermediate dark states with >100 s durations during halide exchange originate from two distinct defect‐mediated reconstruction processes with different activation energies (0.072 and 0.40 eV), leading to an isokinetic temperature of ca. 314 K, across a solid‐state miscibility gap between the I‐ and Br‐rich phases inside a single NC.