Objective To describe the prevalence and epidemiology of congenital polydactyly and syndactyly in Hunan Province, China, 2016-2020. Methods Data were obtained from the Birth Defects Surveillance System in Hunan Province, China, 2016-2020. Prevalence of birth defects (polydactyly or syndactyly) is the number of cases per 1000 births (unit: parts per thousand). Prevalence and 95% confidence intervals (CI) were calculated by the log-binomial method. Chi-square trend tests (chi(2)(trend)) were used to determine trends in prevalence by year. Crude odds ratios (ORs) were calculated to examine the association of each demographic characteristic with polydactyly and syndactyly. Results Our study included 847,755 births, and 14,459 birth defects were identified, including 1,888 polydactyly and 626 syndactyly cases, accounting for 13.06% and 4.33% of birth defects, respectively. The prevalences of total birth defects, polydactyly, and syndactyly were 17.06 parts per thousand (95%CI: 16.78-17.33), 2.23 parts per thousand (95%CI: 2.13-2.33), and 0.74 parts per thousand (95%CI: 0.68-0.80), respectively. Most polydactyly (96.77%) and syndactyly (95.69%) were diagnosed postnatally (within 7 days). From 2016 to 2020, the prevalences of polydactyly were 1.94 parts per thousand, 2.07 parts per thousand, 2.20 parts per thousand, 2.54 parts per thousand, and 2.48 parts per thousand, respectively, showing an upward trend (chi(2)(trend) = 19.48, P < 0.01); The prevalences of syndactyly were 0.62 parts per thousand, 0.66 parts per thousand, 0.77 parts per thousand, 0.81 parts per thousand, and 0.89 parts per thousand, respectively, showing an upward trend (chi(2)(trend) = 10.81, P = 0.03). Hand polydactyly (2.26 parts per thousand vs. 1.33 parts per thousand, OR = 1.69, 95%CI: 1.52-1.87) and hand syndactyly (0.43 parts per thousand vs. 0.28 parts per thousand, OR = 1.42, 95%CI: 1.14-1.76) were more common in males than females. Polydactyly (2.67 parts per thousand vs. 1.93 parts per thousand, OR = 1.38, 95%CI: 1.26-1.51) and syndactyly (0.91 parts per thousand vs. 0.62 parts per thousand, OR = 1.47, 95%CI: 1.26-1.72) were more common in urban areas than in rural areas. Compared to maternal age 25-29, hand polydactyly was more common in maternal age < 20 (2.48 parts per thousand vs. 1.74 parts per thousand, OR = 1.43, 95%CI: 1.01-2.02) or >= 35 (2.25 parts per thousand vs. 1.74 parts per thousand, OR = 1.30, 95%CI: 1.12-1.50). Conclusion In summary, we have described the prevalence and epidemiology of polydactyly and syndactyly from hospital-based surveillance in Hunan Province, China, 2016-2020. Our findings make some original contributions to the field, which may be valuable for future research.