Canine babesiosis is a serious disease among tick-borne haemoprotozoan diseases that threaten dog health. To find out the prevalence of canine babesiosis and its main pathogenic species in Shaanxi Province, the study was centered on the infection of babesiosis in dogs in different regions of the Province. First, a total of 367 blood samples were collected in Shaanxi Province, and 53 Babesia nucleic-acid-positive samples were found by polymerase chain reaction (PCR) identification, with a positive rate of 14.44%, and Babesia gibsoni was found by sequencing analysis. Further analysis showed that the prevalence of canine babesiosis was significantly different in 5 regions. There was no significant difference in infection rates between age groups, with the lowest prevalence in young dogs (10.81%) and the highest in adult dogs (17.29%). The infection rate in male dogs was higher than in female dogs. The morbidity of canine Babesia spp. was significantly different between different seasons, with the highest infection rate in autumn (27.78%) and the lowest in winter (6.10%). In conclusion, the epidemicity of canine Babesia spp. in dogs was mainly affected by region and season, and B. gibsoni was the most common canine Babesia spp. within Shaanxi Province in our study. These results provide basic data for the prevention and control of canine babesiosis in this region.