Anaplasma genus infects the blood cells of humans and animals by biting, causing zoonotic anaplasmosis. However, limited data are available on carrier animals for Anaplasma spp. antibodies in the Qinghai–Tibetan Plateau Area. Therefore, a serological indirect ELISA diagnostic method based on the major surface protein 5 (MSP5), derived from Anaplasma phagocytophilum, was developed in this study to analyze both IgG and IgM antibodies of Anaplasma spp. in a total of 3952 animals from the Qinghai–Tibetan Plateau, including yaks (Bos grunniens), cows (Bos taurus), cattle (Bos taurus domesticus), Tibetan sheep (Ovis aries), horses (Equus ferus caballus), pigs (Sus domesticus), chickens (Gallus gallus domesticus), donkeys (Equus asinus), stray dogs (Canis sp.), and stray cats (Felis sp.). The results showed that recombinant MSP5 protein was expressed and was successfully used to establish the indirect ELISA methods. The overall positivity for Anaplasma IgG and IgM antibodies was 14.6% (578/3952) and 7.9% (312/3952), respectively, and a total of 123 animals (3.1%) were both IgG- and IgM-positive. Moreover, the most prevalent Anaplasma IgG positivity was exhibited by donkeys (82.5%), followed by stray dogs, Tibetan sheep, pigs, chickens, horses, yaks, cows, cattle, and stray cats. The analysis for IgM antibody positivity revealed that IgM positivity was the most prevalent in the stray dogs (30.1%), followed by horses, yaks, Tibetan sheep, cows, stray cats, and cattle. Moreover, the results revealed significant differences (p < 0.05) at different altitudes in Anaplasma-specific IgG in the yaks, Tibetan sheep, and horses, and in IgM in the yaks and Tibetan sheep. In conclusion, this study is the first to demonstrate that yaks, cows, cattle, Tibetan sheep, horses, donkeys, stray dogs, stray cats, pigs, and chickens living in the Qinghai–Tibet Plateau are carrier animals for Anaplasma spp. IgG or IgM antibodies. The current findings provide valuable current data on the seroepidemiology of anaplasmosis in China and for plateau areas of the world.