Thorium (Th) is a naturally occurring radioactive element found in the environment, and recent advancements have been made in identifying and characterizing Th-bearing nanoparticles (NPs). However, the main focus is still on synthesized Th-bearing NPs and knowledge about natural Th-bearing NPs remains limited. Here, high-resolution transmission electron microscopy (HRTEM) observations of thorite from the Huayangchuan uranium ore deposit in Shaanxi Province, Central China, have revealed the nanoscale mineral characteristics of thorite. In this study, thorite NPs ranging from 5–10 nm in size were identified within the uranium ore. A combination of transmission electron microscopy-energy dispersive spectroscopy (TEM-EDS) elemental mapping and corresponding HRTEM images alongside Selected Area Electron Diffraction (SAED) and Fast Fourier Transform (FFT) patterns revealed a complex nanoscale structure in the thorite NPs, consisting of both amorphous and crystalline nanodomains with abundant defects. These nanostructures are associated with a metamictization mechanism in micrometer-sized thorite. Our findings indicate that the metamictization process can generate numerous thorite nanoparticles. Given the high penetrability and mobility of these NPs, the metamictization of thorite poses new challenges for the long-term stability of radioactive substances and the storage containers for radioactive waste. Furthermore, considering the likelihood of environmental release and the chemical toxicity, radioactivity, and nanotoxicity of natural Th-bearing NPs, increased attention should be given to the presence of natural thorite NPs in the ore deposit.