Background: Blastocystis is ubiquitous presence in animals and humans worldwide and has a high level genetic diversity. The aim of this study was to conduct a summary of Blastocystis prevalence, subtypes (STs) in humans and animals in China and depict their distribution.Methods: We searched for the articles related to epidemiology of Blastocystis in humans and animals throughout China which published from January 1, 1990, to July 1, 2019 in the following databases: PubMed, China National Knowledge Infrastructure (CNKI) and Wanfang database. The keywords were Blastocystis and one of the following ones: STs, subtypes, distribution, epidemiology, prevalence, infection, molecular, geographic, intestinal parasites, genetic diversity and characterization.Results: In recent years, various molecular epidemiological studies have been carried out in some provinces/regions of China to identify subtypes of Blastocystis. Infants and young children, school students, hospitalized diarrhea patients, human immunodeficiency virus (HIV) patients, tuberculosis patients, and cancer patients as respondents had been included. ST1–ST7 and ST12 were the main subtypes in Chinese population. Moreover, surveys of Blastocystis infection in animal were also conducted in some provinces. A variety of animals were investigated including pigs, cattle, sheep, yak, giant panda, and Crested ibis (Nipponia nippon), et al., with the main subtypes of ST1–ST8, ST10, ST12–ST14.Conclusion: In recent years, some provinces/regions in China have conducted various molecular epidemiological studies to identify the Blastocystis subtypes. It is important to focus on new subtypes and mixed subtypes of infection, while increasing data on ribosomal alleles. We encourage the scientific community to start research on humans and surrounding animals (including domestic and wild animals) to better understand the possibility of Blastocystis transmission between humans and animals. We call for action among researchers studying intestinal parasitic diseases (Blastocystis), start drawing the subtype of Blastocystis and increase the subtype related to its clinical symptoms.