Objective To investigate the status and molecular epidemiology of hepatitis D virus (HDV) infection in the gathering area of Mongolian population in Inner Mongolia Autonomous Region of China. Methods A total of 230 patients with positive hepatitis B surface antigen (HBsAg) who attended Inner Mongolia International Mongolian Hospital from April 2019 to October 2020 were enrolled, and according to related information, they were divided into hepatitis B+liver cirrhosis group( n =18) and hepatitis B group( n =212). According to HBsAg quantification with a cut-off value of 250 IU/mL, the patients were divided into HBsAg < 250 IU/mL group( n =104) and HBsAg ≥250 IU/mL group( n =126). ELISA was used to detect HDV antibody, and quantitative real-time PCR was used to measure HDV RNA in patients with positive HDV antibody. Genotyping was performed for HDV RNA-positive samples. The chi-square test was used for comparison of categorical data between two groups. Results The positive rate of HDV antibody was 16.09%, and among the patients with positive HDV antibody, the positive rate of HDV RNA was 91.89%. Among the 18 patients with hepatitis B and liver cirrhosis, the positive rate of HDV antibody was 44.44%, and among the patients with positive HDV antibody, the positive rate of HDV RNA was 100%. There were 104 patients with HBsAg < 250 IU/mL, among whom only 3 patients (2.88%) were positive for hepatitis D antibody, and there were 126 patients with HBsAg ≥250 IU/mL, with a positive rate of HDV antibody of 26.98%. Genotype 1 was observed in all the samples that could be genotyped. Conclusion There is a relatively high infection rate of HDV in Inner Mongolia Autonomous Region, especially in patients with HBsAg ≥250 IU/mL or those with liver cirrhosis. It is necessary to strengthen the detection of hepatitis D in HBsAg-positive patients and perform early diagnosis and treatment to prevent the further progression of hepatitis.