Nanoparticles (NPs) are small-sized, with high surface activity and antibacterial and antioxidant properties. As a result, some NPs are used as functional ingredients in food additives, food packaging materials, nutrient delivery, nanopesticides, animal feeds, and fertilizers to improve the bioavailability, quality, and performance complement or upgrade. However, the widespread use of NPs in the industry increases the exposure risk of NPs to humans due to their migration from the environment to food. Nevertheless, some NPs, such as carbon dots, NPs found in various thermally processed foods, are also naturally produced from the food during food processing. Given their excellent ability to penetrate biopermeable barriers, the potential safety hazards of NPs on human health have attracted increased attention. Herein, three emerging NPs are introduced including carbon-based NPs (e.g., CNTs), nanoselenium NPs (SeNPs), and rare earth oxide NPs (e.g., CeO NPs). In addition, their applications in the food industry, absorption pathways into the human body, and potential risk mechanisms are discussed. Challenges and prospects for the use of NPs in food are also proposed.