Si nanocrystal (nc-Si) embedded in SiO2 thin film is synthesized with low-energy Si ion implantation. Depth profiling of the charging effect of the nc-Si is determined from X-ray photoemission measurement. It is observed that there is a strong correlation between the depth profile of the charging effect and the nc-Si depth distribution. The charging effect is found to decrease with the increase of nc-Si concentration and to vanish when a densely stacked nanocrystal layer is formed. The phenomenon is attributed to the charge diffusion among the nanocrystals. The charge diffusion in the nanocrystal layer may have an important implication for nanocrystal flash memory. When such a layer is used as the charge-storage layer in the memory cells, the stored charges could be lost due to the rapid charge diffusion among the nc-Si if a single defect exists in the tunneling oxide, causing a reliability problem in data retention.