Abstract Near‐infrared long‐afterglow nanomaterials hold significant potential in nanomedicine platforms, including targeted drug delivery, precise imaging, and immunotherapy. Improving the particle size distribution and reducing the nanoparticle size to enhance biocompatibility are crucial. Due to the small size effect, reducing the nanoparticle size and improving uniformity typically lead to a decrease in afterglow performance. In this study, near‐infrared long‐afterglow nanoparticles, Zn 2 Ga 2.98 − x Ge 0.75 O 8 :Cr 3+ 0.02 ,Sm 3+ x ( x = 0, 0.02, 0.04, 0.06, 0.08) (ZGGO:Cr 3+ ,Sm 3+ x ), were synthesized using the Sm 3+ ion doping strategy at varying doping concentrations. This work reveals how cation substitution simultaneously affects the nanoparticle size and enhances the near‐infrared long‐afterglow luminescent performance. The Sm 3+ ion doping overcame the increased surface defects caused by the reduced particle size, while simultaneously improving the number of effective luminescent centers by modifying the crystal field environment around the luminescent center. The afterglow intensity and duration of ZGGO:Cr 3+ ,Sm 3+ x nanoparticles were significantly enhanced. The study shows that Sm 3+ ion doping effectively reduces the size of ZGGO:Cr 3+ ,Sm 3+ x nanoparticles while extending the near‐infrared long‐afterglow time by modulating trap depth, the interaction between traps and excited‐state energy levels, and the competition between thermal activation and tunneling processes.