In this study, high-temperature blackening (pile fermentation), a technique originally used for dark tea processing, was applied for the first time to the processing of goji berries (Lycium barbarum L.) to enhance their functional components and antioxidant activity. Single factor experiments were conducted to examine the effects of blackening temperature (60–80 °C), time (40–60 h) and water replenishment (25–45 %) on total phenolic content, flavonoid content, reducing sugar content, DPPH radical scavenging capacity and sensory quality. On this basis, a three factor, three level Box Behnken response surface design was employed to optimize the process, using DPPH radical scavenging capacity as the response value. The results showed that temperature was the dominant factor affecting the quality of blackened goji berries, with the order of influence strength being temperature > water replenishment > time. The established quadratic regression model was significant (P = 0.0011) with a coefficient of determination R² = 0.9473. The optimal process parameters were determined as follows: dried goji berries with a moisture content of 10–13 % were selected, cleaned, supplemented with water to 35 %, and then blackened at 72 °C for 50 h. Under these optimized conditions, the DPPH radical scavenging capacity reached 21.7 μmol/mL, while total phenolic and flavonoid contents remained high, and the sensory evaluation was excellent. This study provides a scientific basis and an industrially applicable technical solution for the high value processing of goji berries.