Capsella bursa-pastoris (cv. Banye) was soaked in 100 μmol/L melatonin solution for 10 min and then stored at 2 ℃. Its quality and antioxidant capacity were evaluated as a function of storage time, and changes in chloroplast ultrastructure in its leaves were observed. The results showed that treatment with 100 μmol/L melatonin significantly reduced the respiration rate, inhibited the degradation of chlorophyll, decreased the accumulation of reactive oxygen species (ROS), and increased the activity of antioxidant enzymes such as superoxide dismutase (SOD), catalase (CAT), peroxidase (POD), and ascorbate peroxidase (APX) and the contents of antioxidants. After 18 days of storage, melatonin-treated Capsella bursa-pastoris showed a 17.3% reduction in respiration rate, a 1.18- and 2.23-fold increase in the contents of ascorbic acid (ASA) and reduced glutathione (GSH), respectively, and a significant increase in the activities of SOD and glutathione reductase (GR) compared with the distilled water-treated control. The ultrastructural observation showed that the shape of chloroplasts and the lamellar structure of chloroplast grana in Capsella bursa-pastoris leaves were maintained well after treatment with melatonin. Therefore, melatonin treatment is beneficial to inhibit the yellowing, maintain the quality of Capsella bursa-pastoris and the structure of chloroplasts, and improve the antioxidant capacity of Capsella bursa-pastoris.