Theileria, Babesia and Cryptosporidium are important parasitic pathogens in cattle. Herein, we carried out this survey to reveal the prevalence and genetic characteristics of four important protozoa in yaks in western China. A total of 1091 serum samples were totally acquired from yaks on the high remote plateau and were assayed for antibodies against Theileria and Babesia by pilot commercial ELISA kits. Eighty-five blood samples and 57 feces were obtained and PCR analyses were performed. The results revealed that the overall prevalence of Theileria, Babesia and mixed Theileria-Babesia infections in yaks was 15.12, 21.54 and 6.51%, respectively. Four out of 85 blood samples were observed to be PCR-positive for Babesia bigemina (B. bigemina) with 99.77% similarity to the MK587709.1 isolate. Among the 57 fecal samples, five samples tested positive for C. parvum (IId genotype), while one sample tested positive for C. hominis. Our study provides a solid theoretical basis for the need to prevent infections of animals by those protozoa in order to improve yaks’ productivity on the Qinghai Tibetan plateau.