The crystal structure and phase stability of a host lattice plays an important role in efficient upconversion phenomena. In stable hosts, lanthanides doping should not generally change the crystal structure of the host itself. But when phase of a system drastically changes after lanthanide doping resulting in multiple phases, accurate identification of upconverting phase remains a challenge. Herein, an attempt to synthesize lanthanide‐doped NiMoO4 by microwave hydrothermal method produced MoO3/Yb2Mo4O15/NiMoO4 micro‐nano composite upconversion phosphor. A combined approach of density functional theory (DFT) calculations and single‐particle‐level upconversion imaging has been employed to elucidate the phase stability of different phases and upconversion properties within the composite. Through single‐particle‐level imaging under 980 nm excitation, an unprecedented resolution in visualizing individual emitting and non‐emitting regions within the composite has been achieved, thereby allowing to accurately assign the Yb2Mo4O15 as a sole upconversion emitting phase in the composite. Result of the DFT calculation further shows that the Yb2Mo4O15 phase is the most thermodynamically preferred over other lanthanide‐doped phases in the composite. This comprehensive understanding not only advances the knowledge of upconversion emission from composite materials but also holds promise for tailoring optical properties of materials for various applications, including bioimaging, sensing, and photonics, where controlled light emission is crucial.