The bulb of Lilium lancifolium, a traditional Chinese medicine and food-homologous material, is rich in various saponins with notable pharmacological activities. However, traditional extraction methods using single solvents suffer from low efficiency, high cost, and flammability. To address these limitations, this study developed a green and efficient extraction method using natural deep eutectic solvents (NADES). Twenty-four NADES were synthesized and screened for stability, leading to the selection of fourteen for subsequent extraction of saponins from L. lancifolium, with ethanol extraction as a control. Through optimization, NADES-15, composed of choline chloride and anhydrous citric acid (2:1), was identified as the most effective solvent. Quantitative analysis revealed that the total saponin content obtained with NADES-15 (46.6 mg/g) significantly surpassed that of ethanol. Furthermore, UHPLC-MS/MS analysis demonstrated a greater diversity of chemical components in the NADES-15 extract, wherein 31 compounds were tentatively identified, including all nine target steroidal saponins (lily saponin A–I), compared to only 17 compounds and six saponins found in the ethanol extract. This study highlights the significant advantages of NADES in enhancing both the efficiency and variety of active component extraction from L. lancifolium, offering a novel and green approach for natural product extraction.