The efficient and green extraction of bioactive ingredients from natural plants play a vital role in their corresponding drug effects and subsequent studies. Recently, deep eutectic solvents (DESs) have been considered promising new green solvents for efficiently and selectively extracting substances from varied plants. In this work, an environment-friendly DESs-based ultrasonic-assisted extraction (DESs-UAE) procedure was developed for highly efficient and non-polluting extraction of alkaloids from the roots of Stephania tetrandra (ST). A total of fifteen different combinations of DESs, compared with traditional organic solvents (methanol and 95% ethanol) and water, were evaluated for extraction of bioactive alkaloids (FAN and TET) from ST, and the results revealed that DESs system made up of choline chloride and ethylene glycol with mole ratio of 1:2 exhibited the optimal extraction efficiency for alkaloids. Additionally, a four-factor and three-level Box-Behnken design (BBD), a particular pattern of response surface methodology (RSM), was used to optimize extraction conditions. RSM results indicated that the maximum extraction yields of FAN, TET, and TA were attained 7.23, 13.36, 20.59 mg/g, respectively, within extraction temperature of 52 °C, extraction time of 82 min, DES water content of 23% (v/v), and liquid-solid ratio of 23 mL/g. The measured results were consistent with the predicted values. Notably, the optimized DES extraction efficiency of TA, according to the experimental data analysis, is 2.2, 3.3 and 4.1 times higher than methanol, 95% ethanol and water, respectively. Meanwhile, based on 3D response surface plots, interactive effects plots and contour maps, the effects of the aforementioned four essential factors on the extraction yield and their interactions on the response were visualized. The results revealed that the mutual interactions between extraction temperature and liquid-solid ratio exhibited positive effects on all responses, while extraction time and water content in DES posed a negative effect. Therefore, these results suggest that DESs, as a class of novel green solvents, with the potential to substitute organic solvent and water, can be widely and effectively applied to extract bioactive compounds from natural plants.