Lanthanides (Ln³⁺) doped luminescent materials play critical roles in lighting and display techniques. While increasing experimental and theoretical research have been carried out on aluminate-based phosphors for white light-emitting diodes (WLEDs) over the past decades, most investigation was mainly focused on their luminescent properties; therefore, the local structure of the light emission center remains unclear. Especially, doping-induced local composition and structure modification around the luminescent centers have yet to be unveiled. In this study, we use advanced electron microscopy techniques including electron diffraction (ED), high-resolution transmission electron microscopy (HRTEM), high-angle annular dark-field scanning transmission electron microscopy (HAADF-STEM), in combination with energy dispersive X-ray spectroscopy (EDX) and electron energy loss spectroscopy (EELS), to reveal atomically resolved crystalline and chemical structure of Ce³⁺ doped CaYAlO₄. The microscopic results prove substantial microstructural and compositional inhomogeneities in Ce³⁺ doped CaYAlO₄, especially the appearance of Ce dopant clustering and Ce³⁺/Ce⁴⁺ valence variation. Our research provides a new understanding the structure of Ln³⁺ doped luminescent materials and will facilitate the materials design for next-generation WLEDs luminescent materials.