Objective: To investigate the prevalence of hepatitis B and hepatitis C in Hotan Prefecture, Xinjiang Uygur Autonomous Region, so as to provide insights into prevention and intervention strategies for viral hepatitis for these populations. Methods: Data on hepatitis B and hepatitis C cases in Hotan Prefecture from 2016 to 2022 were collected through the Chinese Disease Prevention and Control Information System. The temporal, demographic and regional distribution characteristics of hepatitis B and hepatitis C incidence were analyzed using the descriptively epidemiological method. The trends in the incidence of hepatitis B and hepatitis C from 2016 to 2022 were analyzed using average annual percent change (AAPC). Results: A total of 8 910 hepatitis B cases and 4 106 hepatitis C cases were reported in Hotan Prefecture from 2016 to 2022, with average annual incidences of 55.60/105 and 25.61/105, respectively. The average annual incidence of hepatitis B in males was 66.78/105, which was higher than that in females (43.83/105, P<0.05). The average annual incidence of hepatitis C in males was 25.70/105, while in females it was 25.36/105, with no statistically significant difference (P>0.05). With increasing age, the incidence of hepatitis B showed an "M"-shaped trend, with the highest average annual incidence in the age group of 20-<30 years (97.20/105); the incidence of hepatitis C first increased and then decreased, with the highest average annual incidence in the age group of 70-<80 years (102.50/105). The majority of the cases were farmers/migrant workers, with 5 610 (62.96%) and 2 963 cases (72.16%), respectively. The top three counties with higher average annual incidences of hepatitis B were Minfeng County (84.78/105), Karakax County (81.69/105) and Lop County (72.20/105), and the top three counties with higher average annual incidences of hepatitis C were Pishan County (46.92/105), Karakax County (35.62/105) and Hotan County (26.31/105). The incidences of hepatitis B and hepatitis C in Hotan Prefecture showed downward trends from 2016 to 2022 (AAPC=-10.711% and -16.594%, both P<0.05), with consistent trends observed in Hotan City, Hotan County, Pishan County and Qira County (all P<0.05). Conclusions From 2016 to 2022, the incidences of hepatitis B and hepatitis C in Hotan Prefecture both showed downward trends. Young and middle-aged adults, males, and farmers/migrant workers were the high-risk populations for hepatitis B, while middle-aged and elderly adults and farmers/migrant workers were the high-risk populations for hepatitis C.