The observed photoluminescent properties of Ce3+-doped NaK2Li[Li3SiO4]4 suggest the importance and potential of this phosphor in practical applications. It is noted that only half of the Na+ and Li + sites in the Na/Li channel are found to be occupied in the host and two sets of different luminescent Ce3+ centers are observed. In this work, first-principles calculations are performed to resolve the site occupancy of Ce3+ by taking experimental synthesis conditions into consideration. The formation energy results show that Ce3+ prefers to replace the Na atom in the Na/Li channel than K atom in the K channel, whilst the cation vacancies VLi, VNa and VK are formed as charge compensation. Besides, a large amount of Ce4+ would be present. Based on the obtained excitation and emission energies, the Stokes shifts, and the 5d crystal-field splitting, the luminescent center with a larger red-shift of the emission wavelength is assigned as Ce at the Na site, and the other center is assigned as Ce at the K site. The energy level structures of Ce occupying a certain site (Na site or K site) with different local environments differ slightly, thus the broadening of the spectra can be interpreted. Furthermore, we provide an explanation on the excellent thermal stability of this phosphor based on the large energy barrier for the 5d-4f crossover point and the large 5d thermal ionization energy. To sum up, the insights gained in this work deepen our understanding on the luminescent properties of Ce3+-doped NaK2Li[Li3SiO4]4 in which some of the host cation sites are partially occupied.