Three dimensional (3D) flower-shaped microarchitectures of NaY(WO4)2 were synthesized via a microwave-assisted hydrothermal process in the presence of trisodium citrate (Na3Cit) and a post-calcination process. The effects of reaction conditions on the morphology of precursor microstructures were studied. It was found that Na3Cit, as the chelating agent and shape modifier, plays a key role in the microstructure growth. A possible growth mechanism for the flower-shaped microarchitectures was proposed. The as-formed precursor can completely transform into NaY(WO4)2 with its original flower-shaped morphology via a heat treatment process. The concentration and temperature quenching behaviors of Eu3+ fluorescence in the flower-shaped NaY(WO4)2 were studied, and the optimal doping concentration was confirmed, meanwhile the activation energy was obtained. Judd-Ofelt parameters Ωλ (λ = 2, 4 and 6) of Eu3+ in the flower-shaped NaY(WO4)2 phosphor were obtained by using the emission spectrum of Eu3+, moreover the radiative transition properties were analyzed.