AbstractRecently, study on Cr3+‐doped zinc gallate and zinc gallogermanate persistent phosphors has become a hot topic in persistent luminescence and bio imaging areas, because of their near infrared (NIR) emission and long afterglow. However, regulation of efficient traps and improvement of persistent luminescence through bottom‐up design are the key challenge. Here, we recommend a new paradigm of chemical unit co‐substitution with [Mg2+‐Ge4+] substituting for [Ga3+‐Ga3+] in ZnGa2O4, which contributes to the opposite charged and distorted octahedral defects of MgGa′ and GeGa· in pair around the CrN2 ions. The formed defect clusters of MgGa′‐CrN2‐GeGa·, which are closely related to the trap depth, can be accurately regulated through varying the doping content of Mg2+/Ge4+ in the resulting spinel solid solutions of ZnGa2−x(Mg/Ge)xO4:Cr3+ (x = 0–1.25). Moreover, the defect clusters cannot only store and recharge visible and UV radiations that contributes to the long lasting NIR persistent luminescence but also can enhance the NIR emission intensity at ~695 nm. The persistent luminescence induced by UV light excitation exhibits an improvement at a deeper trap depth, but it follows an opposite law through visible light excitation. The prepared nanoparticles have the advantages of intense NIR emission, long lasting afterglow, and excellent rechargeability for visible/UV radiations, so they are the potential nanoprobes for long‐term bio imaging in living animals.