In this work, radioluminescence (RL), thermoluminescence (TL) and photoluminescence (PL) of fluorophosphate Li9Mg3[PO4]4F3 as a possible dosimetry material are studied for the first time. It was found that the irradiated sample exhibits significant thermoluminescence in the temperature range of 100–300°С with the main peak at 205°С. The RL, PL and TL spectra consist of one broad band centered at 400 nm which was attributed to defects in the structure of Li9Mg3[PO4]4F3. The energy required to excite defects in Li9Mg3[PO4]4F3 determined by UV–vis spectroscopy is 4.4 eV (λ ≈ 280 nm). Additional evidence for intrinsic defects was obtained from the electron paramagnetic resonance (EPR) in Li9Mg3[PO4]4F3. The DFT method was employed to simulate various defects including single and complex, neutral and charged vacancies. The formation energies of vacancies were predicted and their effect on the electronic structure and optical properties was established. These intrinsic defects introduce additional electronic states into the band gap and absorption bands in the visible region, the position and intensity of which strongly depend on the type of defect. Our experimental and theoretical studies reveal that Li9Mg3[PO4]4F3 can be a promising optical matrix suitable for dosimetric applications. As evidence, the main functional characteristics of the new material are given.