Natural deep eutectic solvents (NADES) were successfully employed as green alternatives to the traditional ones for the extraction of chlorogenic acid from herba artemisiae scopariae. Significantly, the method of solvent effect theory chemical calculation assistance to guide the NADES selection for the extraction was proposed. Proline–malic acid was successfully screened as the suitable solvent using the calculation results and it gave the best chlorogenic acid yield of 3.77 mg g⁻¹ among the NADES tested with a solvation free energy of −5.86 × 10⁶ kJ mol⁻¹ from the calculation. The calculation-assisted method saves costs and material resources for the applications of the green alternative NADES and provides a research route that can be used for the extraction of target active molecules in the traditional Chinese medicine and food industry.