Abstract: To investigate the green aqueous extraction process of chromoplasts from goji berries, fresh fruits were used as raw materials, and single-factor experiments were conducted to examine the effects of extraction solvent, solid-liquid ratio, and filter cloth pore size on chromoplast yield and pigment content. High-performance liquid chromatography (HPLC) was employed to identify the pigment composition of the obtained chromoplasts, which were further purified using sucrose gradient solutions. The solubility and rehydration capacity of the purified chromoplasts were also evaluated. The results showed that using PBS buffer as the extraction solvent, with a solid-liquid ratio of 1:10 (w/v, g/mL) and filtration through a 40-mesh filter cloth, achieved the highest chromoplast yield (69.32%) and pigment content (5.75%). The extracted chromoplasts contained zeaxanthin, zeaxanthin monopalmitate, and zeaxanthin dipalmitate at levels of 57.93±5.89, 77.62±17.58, and 5609.50±113.14 mg/100 g, respectively, with no significant difference compared to their proportions in fresh goji berries. Combined optical microscopy and TEM observations confirmed that the extracted chromoplasts exhibited high structural integrity. After purification with 30% sucrose gradient, the pigment content increased significantly to 11.3% (P<0.05), and the chromoplasts showed improved integrity and dispersion uniformity. Comparison of the solubility of pigments extracted by organic solvents with chromoplasts obtained by green aqueous extraction revealed that the latter possessed dual advantages of both lipid and water solubility. This study provides a novel approach for the green extraction of goji pigments, establishes a foundation for the application of chromoplasts as water-soluble colorants, and offers new insights into utilizing lipid-soluble bioactive compounds in foods through their natural carrier systems.