Objective Though HCV genotyping , liver ultrasound and liver function indicators were used to assess the relationship between HCV genotyping, viral RNA copy number and liver damage related indicators in patients with chronic hepatitis C. Methods A total of 105 Uyghur hepatitis C patients in Aksu, Xinjiang were recruited in our hospital. All patients were carried out a test of HCV RNA copy number. HCV genotyping was performed by fluorescence quantitative PCR method. Fully automatic biochemical analyzer was used for alanine aminotransferase (ALT), aspartate aminotransferase (AST), direct bilirubin (DIBL) and total bilirubin (TIBL) by commercial kits. Color doppler ultrasound system was used for liver ultrasound. Results The genotyping results of 105 Uyghur hepatitis C patients showed that type 1b, 2a, 3a, 3b and 6a were 46, 41, 8, 8 and 2, respectively. Type 1b was the main type of HCV virus. The proportion of RNA copy number, AST and ALT levels, and liver cirrhosis were higher in patients with type 1b. Statistical analysis showed that there was a significant correlation between different HCV virus types and HCV RNA copy number (P = 0.032). In terms of AST and ALT levels, there were significant differences between type 1b, type 2a and other genotypes (type 3b and type 3a and type 6a) (P < 0.01). In addition, patients with normal liver, enlarged liver spots, fatty liver and cirrhosis have significant differences among type 1b, type 2a and other genotypes (P < 0.01). Conclusion There are regional differences in HCV genotyping among Uygur people in Aksu, Xinjiang. HCV RNA copy number and degree of liver damage are correlated with different HCV genotypes, which is of great significance to guide the clinical diagnosis and treatment of HCV in local populations.