Blastocystis is a common intestinal protist in humans and animals. Currently, Blastocystis infection in bar-headed geese is unknown. To understand the prevalence and distribution of Blastocystis subtypes in bar–headed geese, fecal samples were collected from 358 bar–headed geese in three regions. The total infection rate of Blastocystis in bar–headed in China was 5.9% (21/358), with 5.0% (6/120) in Aba (Ngawa) Tibetan and Qiang Autonomous Prefect, Sichuan province, 11.8% (14/119) in Maqu county, Gansu province, and 0.8% (1/119) in Caohai, Wei ning county, Guizhou province. The differences in prevalence rates by region were statistically significant. Sequences analyses showed that one known subtype (ST7, n = 16) and one potentially novel ST (n = 5) in bar–headed geese were detected in this study. This is the first report on the prevalence and subtype distribution of Blastocystis in bar–headed geese, which will improve our understanding of the epidemiology and public health implications of Blastocystis infection in wild migratory birds.