Natural deep eutectic solvents (NaDESs) are considered a new type of green solvent with attractive application prospects in many fields because of their simple preparation, low cost, environmental friendliness, low volatility, high solvency capacity, designable structure, and easy biodegradability. Due to their biocompatibility, they are safe to use and are particularly suitable for natural product applications. In recent years, NaDESs have been used to extract phytonutrients (e.g., flavonoids, saponins, polysaccharides, alkaloids, quinones, phenolic acids, volatile oils, etc.) to improve their solubility, stability, and bioavailability. This review is intended to summarize and discuss recent progress in the field of natural products related to materials and preparation methods, physicochemical properties, enhancing extraction and separation, increasing solubility, improving stability and bioavailability, facilitating oral absorption of phytonutrients, and finally, highlighting the challenge for future work.