The critical doping structures of rare-earth atoms in the promising β-SiAlON phosphors have long been argued owing to the lack of direct evidence. Here, the exact locations and coordination of the Ce rare-earth atoms in the β-SiAlON structure have been examined using an atom-resolved Cs-corrected scanning transmission electron microscope. Three different occupation sites for the Ce atoms have been directly observed: two of them are in the structural channel coordinated with six and nine N(O) atoms, respectively; the other one is the unexpected substitution site for Si(Al). The chemical valences and stabilities of the doping Ce ions at the different occupation sites have been evaluated using density functional calculations. Correlation of the different doping structures with the luminescence properties has been investigated by the aid of cathodoluminescence (CL) microanalysis, which verifies the different contribution of the interstitial trivalent Ce ions to the light emission while no luminescence is observed for the substitutional doping of quadrivalent Ce.