Background: Thumb polydactyly is one of the commonest congenital hand differences. Traditional surgeon-based outcome scores capture outcomes mainly on bodily structure and function. Outcomes on the long-term well-being of the patients in the domains of activity and participation are not fully studied. Methods: Forty-eight thumbs in forty-five Chinese patients with radial polydactyly underwent surgical treatment at or before 3 years old were recruited. Mean follow-up was 11.6 years. Surgical outcomes were collected and compared to the normal opposite thumb. The results were compiled into the Japanese Society for Surgery of the Hand (JSSH) score, Cheng score and Tada score. Patients’ activity involving hands were assessed by both objective tools and patient-reported outcome measure while their health-related quality of life (HRQoL) was assessed by Patient- and Parent-reported Pediatric Quality of Life Inventory (PedsQL). Correlations between outcomes were analysed. Results: Overall, both parents and patients themselves reported good quality of life with mean score of 86.6% and 92.1% respectively in PedsQL. The combined surgical scores ranged from 52% good or excellent results using JSSH score to 100% good result using Cheng score. None of the outcomes on bodily structure and function showed positive correlation with patient’s well-being. Negative correlation was noted in total passive range of movement, active movement and Cheng score. All patients reported no activity restriction. Writing test did not show significant slowing. The operated hands had significantly poorer fine motor dexterity than normal. No significant correlation is noted between activity outcomes and PedsQL. Conclusions: Outcomes on bodily structure, function and activity showed little correlation with patients’ well-being after thumb polydactyly correction. It should be careful in using or analysing patient/parent-reported outcome measures on HRQoL as outcome assessment of surgical treatment of radial polydactyly.