There are abundant natural products resources and extensive clinical use experience in China. However, the active components of natural products generally have problems such as poor water solubility and low bioavailability, which limit their druggability. Carrier-free nanoparticles, such as nanocrystals, self-assembled nanoparticles, and extracellular vesicles derived from both animal and plant sources, have great application potential in improving the safety and efficacy of drugs due to their simple and flexible preparation methods, high drug loading capacity and delivery efficiency, as well as long half-life in blood circulation. It has been widely used in biomedical fields such as anti-tumor, anti-bacterial, anti-inflammatory and anti-oxidation. Therefore, based on the natural products that have been used in clinic, this review focuses on the advantages of carrier-free nanoparticles in delivering active compounds, in order to improve the delivery process of natural products in vivo and improve their draggability.