A highly efficient and environment-friendly extraction technology was established to extract and enrich multiple amino acids (AAs) in situ by deep eutectic solvent (DES)-assisted mechanochemical extraction (MCE) and aqueous two-phase system (ATPS). Firstly, the DES was prepared from betaine and ethylene glycol in a 1:2 M ratio. Then, a series of conditions were evaluated by single-factor and multifactor experiments to select the optimum experimental parameters. The highest extraction yields of AAs were obtained by DES-assisted MCE and ATPS enrichment, including that the amount of DES was 0.97 mL, the milling time was 4.88 min, the amount of salt was 8 g, and the solid-to-liquid ratio was 0.055 g mL−1. After extracting, the diluted AA extracts were analyzed by a high-performance liquid chromatography-fluorescence detector after pre-column derivatization with 6-aminoquinolyl-N-hydroxysccinimidyl carbamate. The methodological validation demonstrated the proposed method exhibited satisfactory limits of detection ranged from 0.11 to 0.82 ng mL−1, reliable interday precision (%RSD) of 0.014–0.067 % for retention time and 1.29–3.34 % for the peak area, acceptable reproducibility with %RSD below 4.1 %, and good %recovery between 90.3 % and 122.5 % at three spiked concentrations. The surface morphology of raw, only ground, and DES-ground sample powders was tested by scanning electron microscopy to further explore the changes in the physicochemical properties of samples. By comparing with other AAs extraction methods, the developed method is not only eco-friendly, but greatly improves the yield of free AAs extracted from chrysanthemum.