Brazilian blue apatite is highly valued in gemology for its distinctive neon-blue coloration, yet its chromogenic mechanism remains incompletely understood. This study systematically investigated the color origin through conventional gemological testing, Fourier-transform infrared spectroscopy (FTIR), laser Raman spectroscopy, UV-Vis-NIR absorption spectroscopy, laser ablation–inductively coupled plasma mass spectrometry (LA-ICP-MS), and heat treatment experiments. The samples were identified as fluorapatite with [CO₃]²⁻ substituting for [PO₄]³⁻. LA-ICP-MS revealed light rare-earth element (LREE) enrichment, heavy REE (HREE) depletion, and negative Eu anomalies, indicating formation under reduced oxygen fugacity conditions. A positive correlation (R² > 0.8) was observed between LREE concentration and color saturation.Transition metals: Mn³⁺ (absorption at 580-650 nm) serves as the primary chromophore, with Mn content positively correlating with color intensity. Fe³⁺ enhances brightness by suppressing red-light absorption. Rare earth elements, such as Nd³⁺, contribute to red-region absorption (745/801 nm), while Ce³⁺-SiO₃⁻ radicals and SO₃⁻ electron centers dominate UV/blue/green absorption. Excessive Ce³⁺ was found to inhibit blue coloration. Th content indicates the presence of SO₃⁻/SiO₃⁻ radicals. Post-heating color fading (threshold at 400°C) results from U decay-induced color center destruction. Blue-purple fluorescence originates from Ce³⁺ (400 nm emission via 5d→4f transitions) and Eu²⁺ (585 nm), with sharp peaks near 600 nm attributed to Sm³⁺/Pr³⁺ transitions. This study elucidates the synergistic effects of Mn³⁺/Fe³⁺, REE electronic transitions, and color centers in generating the characteristic blue coloration, providing fundamental insights for gemological identification and enhancement protocols.