In the current work, YAGG:Cr3+ nanophosphors were synthesized by the Pechini method and then annealed at different temperatures in the range 800–1300 °C. The structure and morphology of the samples were characterized by X-ray Powder Diffraction (XRPD). The lattice parameters and average crystalline sizes as site occupation by Al3+ and Ga3+ ions were calculated from the Rietveld refinement data. To investigate the effect of crystalline size of the materials on their optical properties: excitation and emission spectra were recorded and analyzed. Finally, the effect of crystalline size on the probability of carrier recombination leading to PersL was determined experimentally with thermoluminescence analyses. The Tmax-Tstop method was applied to determine the trap type and particle size (calcination temperature) effect on their redistribution. A correlation between structural changes and trap redistribution was found. In particular, the extinction of high-temperature TL maximum with increasing annealing temperatures is observed, while low-temperature TL maximum increases and reaches a maximum when the lattice parameter reaches saturation.