Solid-state nuclear magnetic resonance (NMR) spectroscopy serves as a powerful technique for probing local structures. However, the interpretation of NMR signals mainly based on empirical knowledge could lead to imprecise local structural determinations. To address this, density functional theory (DFT)-based theoretical NMR calculations, aided by experimental three-dimensional continuous rotation electronic diffraction (3D cRED) technique, were performed for ZnxY1-xBO3-0.5x borate oxide ion conductors. The calculations provided fine local structure identification for the experimental 11B NMR spectra of ZnxY1-xBO3-0.5x, providing rich information on multiple experimental 11B NMR signals towards the complex boron oxide anions associated with bridging oxygen vacancies and the coexistence of the monoclinic (C2/c), hexagonal (P63/m), and trigonal (R32) phases in ZnxY1-xBO3-0.5x. Owing to the advantages of solid-state NMR in identifying closely related phases compared to X-ray/neutron diffraction technique, along with the advanced 3D cRED technique that allows for rapid phase identification and structure determination, we provide a fine local structure identification and a more inclusive insight into the coexistence of multiple phases in borate with the same composition. More importantly, this work provides guidance for phase and property modulation. Phase modulation in ZnxY1-xBO3-0.5x was carried out with thermodynamic and kinetic modulation and eventually realized the tuning of the local structures and the resultant oxide ion conductivity of ZnxY1-xBO3-0.5x. This work provides a theoretical and experimental platform to access the flexible structural assignment of boron oxide anions and therefore offers new guidance and insights into the defect structures and the phase-property modulation of inorganic solid functional materials beyond borate oxide ion conductors.