Few comprehensive studies have investigated viraemia caused by human parvoviruses (HPAVs) in China. A total of 1626 of blood samples were collected from non-HBV and HBV infected Chinese subjects (adults, N = 1279; children, N = 347) from south-western and south-eastern China. DNA from three HPAVs was detected in blood samples using PCR-based assays. The epidemiological profiles and association with HBV co-infection were also analysed. Of the 1626 blood samples tested, 138 (8.49%) were found to exhibit HPAV viraemia, including 3.51% with B19, 3.75% with HBoV and 2.52% with PARV4. The presence of B19 DNA in both child and adult, as well as that of PARV4 DNA in adult,from the south-western region was significantly higher than that from the south-eastern region (P = 0.006 for B19 in children; P = 0.026 for B19 in adults; and P = 0.014 for PARV4 in adult).However, the frequency of HBoV DNA in adults from the south-western region was significantly lower than that observed in adults from the south-eastern region (P = 0.001). Furthermore, HBoV was more prevalence in male (4.9%) than in female (1.4%) individuals. In addition, no significant correlation between HBV and HPAV co-infection was found using serum samples from Chinese adults. In conclusions,the molecular prevalence of three HPAVs in blood samples exhibited variation among different populations depending on area, age and gender; No association between HPAV and HBV infection in adults was found. Our data provide a basis for improving blood safety and preventing HPAV infection in China.