Chromium-doped persistent luminescence nanoparticles (PLNPs) have promising biomedical applications in X-ray charged near-infrared (NIR) luminous imaging. The persistent luminescence (PersL) property was usually adjusted by co-doping with other ions. Impurity phases were thought to be adverse to the PersL. In this study, a composite material, LiInSi2O6:Cr,Pr·2SiO2 (LICP-S), was synthesized with a PersL peak at 800 nm after being charged by 1 Gy X-ray while LiInSi2O6:Cr (LIC) and LiInSi2O6:Cr,Pr (LICP) possessed no or very weak PersL. Distinctively, excess metastable cristobalite silica was found essential for the much more intense PersL of LICP-S than LICP and LIC. Thermostimulated luminescence spectra studies indicated that cristobalite adjusted the Pr-related traps from deep traps to shallow ones, which facilitated the room temperature PersL. The low dose X-ray charged PersL of LICP-S was applied to demonstrate the luminous labeling of a medical silicone prosthesis that was supposed to be imbedded in body for years via X-ray activated PersL imaging in vitro and in vivo. This work not only provides a kind of PLNPs with 800 nm emission suitable for low dose X-ray activation, but also an unusual strategy for trap engineering in PersL materials by designing multi-phase composites.