Lead-free metal halide nanocrystals (NCs) have aroused increasing attention due to their unique optoelectronic properties based on localized excitons (LEs). However, the vital influencing factors for the LEs based photoluminescence (PL) are still not well-understood due to the coupling of various intrinsic and extrinsic factors of the NCs. Herein, by engineering the phase, size, morphology, and chemical composition, we are able to decouple the intrinsic and extrinsic factors of manganese doped cesium zinc halide NCs. We found both the intrinsic metal-halide coordination field and the extrinsic crystal defects have significant influences on the LEs' recombination and energy transfer processes, and hence determine the PL efficiency. Unlike for the free excitons (FEs) based PL, the phase as well as the crystal morphology do not play major roles for the LEs based PL. This work provides a new insight for the study of LE dynamics of metal halide NCs.