Natural deep eutectic solvents (NADESs), composed of natural primary metabolites, are now widely used as green and sustainable extraction solvents of bioactive components. In the present study, various NADESs were prepared to extract multi-components from different preparations of an herbal formula (Chinese name: Jinqi Jiangtang, JQJT) using ultrasound-assisted extraction (UAE). Results showed that most prepared NADESs provided more effective extraction of phenolic acids and alkaloids from JQJT preparations than conventional solvents. Among the tested NADESs, the solvent formed by choline chloride and laevulinic acid was selected to optimize the operational parameters using response surface methodology. The optimized extraction method was successfully applied to extract six major components in four commercial JQJT products, and quantification analysis was performed by the validated high-performance liquid chromatography with ultraviolet detection (HPLC-UV) method. The quantitative results indicated that preparations from different manufacturers showed different chemical profiles. In conclusion, NADESs-based UAE shows considerable potential as an efficient and green method for extraction of multi-bioactive components from commercial herbal preparations.