Pasteurization usually has a great influence on yogurt and astaxanthin. This study aimed to investigate the effects of 3 pasteurization methods, including 63°C for 30 min (LTLT-1), 65°C for 30 min (LTLT-2), and 75°C for 15 s (HTST), on the physicochemical properties, stability, and biological activity of set yogurt fortified with astaxanthin-rich yolk. The results showed that the LTLT-2 group had a higher astaxanthin retention, with no significant difference from the LTLT-1 group. The in vitro digestion results also confirmed that LTLT-2 had a high free radical scavenging capacity. Temperatures between 63°C and 65°C are within a safe range for preventing significant heat degradation of astaxanthin. Over the 21-d storage period, LTLT-2 significantly outperformed LTLT-1 and HTST regarding texture and particle size. This work demonstrates that the pasteurization conditions of 65°C for 30 min could be used to prepare a functional set yogurt with stable quality and antioxidant activity.