Blastocystis sp., a unicellular intestinal parasite in humans and animals worldwide, is frequently found in immunocompromized patients and people in close contact with animals. Here, we reviewed recent studies on the prevalence, subtypes, and distribution of Blastocystis infection in humans and animals in China. To date, more than 12 provinces have reported Blastocystis infection in humans, with identification of six different subtypes (ST1, ST2, ST3, ST4, ST5, and ST6). The overall infection rate reported was 3.37% (3625/107,695), with the lowest prevalence (0.80%) in Fujian province and the highest prevalence (100%) in Guangdong province. ST3 (62%, 186/300) was the most dominant subtype, identified in all tested provinces in China. A total of eight provinces have reported Blastocystis infection in various animals, with the overall prevalence being 24.66% (1202/4874). Molecular analysis revealed 14 subtypes that infected animals, including 10 known (ST1, ST2, ST3, ST4, ST5, ST6, ST7, ST10, ST13, ST14), and 4 novel (Novel1, Novel2, Novel3, Novel4) subtypes. ST5 was the dominant subtype infecting artiodactyls (44.1%, 460/1044), while ST1 commonly infected carnivores (45.5%, 5/11). These findings provide insights into the epidemiological behavior of Blastocystis sp. in China, and could help in developing effective control strategies against the parasite.