By incorporating the hydrophobic deep eutectic solvents (DESs) into the three-phase partitioning (TPP) technique, a TPP-based method was developed to extract the chia seed polysaccharide (CSP) from chia seed. Through a single-factor experiment and response-surface model, the optimal condition for the TPP extraction was determined as DES composed of dodecanoic acid and octanoic acid in a 1:1 M ratio, (NH4)2SO4 concentration of 32.86 %, crude extract–DES ratio of 0.93 (v/v), aqueous phase pH of 4.38, extraction temperature of 35 °C, and extraction time of 10 min. The polysaccharide yield of the constructed TPP method is 8.65 %, which is higher than the conventional water extraction method (yield is 6.96 %). Molecular dynamics simulations reveal the phase behavior of proteins and polysaccharides in the TPP system, showing that noncovalent interactions play a crucial role in the TPP system. The CSP obtained by the TPP method exhibits distinctive composition, structural, physicochemical, and functional properties, leading to improved thermal stability, rheological behavior, and antioxidant performance. Compared with the traditional extraction method, efficient extraction of CSP can be achieved flexibly using the proposed TPP approach, resulting in high yield and quality of CSP, which provides a new path for the large-scale utilization of chia seed.