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<i>Melophagus ovinus</i> (sheep ked) is a hematophagous ectoparasite that mainly parasitizes sheep. In addition to causing inflammation, wool loss, and skin damage to the animal hosts, <i>M. ovinus</i> also serves as a vector for a variety of pathogens and is highly likely to participate in the life and transmission cycle of pathogenic organisms. Herein, we investigated the presence and molecular characterization of vector-borne pathogens in <i>M. ovinus</i> from Qinghai-Tibet Plateau, China. A total of 92 <i>M. ovinus</i> pools collected from the Qinghai province of China were screened for the presence of selected vector-borne pathogens. The overall positive rate of <i>A. ovis</i>, <i>A. bovis</i>, <i>A. phagocytophilum</i>, and <i>T. ovis</i> in <i>M. ovinus</i> was 39.1%, 17.4%, 9.8%, and 89.1%, respectively. All of the samples were negative for Border disease virus (BDV), other <i>Anaplasma</i> species, <i>Babesia</i> spp., <i>Rickettsia</i> spp., and <i>Borrelia</i> spp. Co-infection of different <i>Anaplasma</i> species and <i>T. ovis</i> occurred in 51.2% of all samples with <i>T. ovis</i>. The positive rates of <i>A. ovis</i>, <i>A. bovis</i>, and <i>A. phagocytophilum</i> in different regions and altitudes of the sampling sites were significantly different. Sequence and phylogenetic analysis of target genes confirmed their identity with corresponding pathogens. Our results elucidate the occurrence and molecular characterization of <i>Anaplasma</i> spp. and <i>Theileria</i> spp. in <i>M. ovinus</i>, which could act as potential zoonotic reservoirs. To the best of our knowledge, this is the first report of the detection of <i>A. bovis</i> and <i>A. phagocytophilum</i> DNA in <i>M. ovinus</i>. This study gives the first extensive molecular survey of vector-borne pathogens with veterinary and public health significance in <i>M. ovinus</i> from the Qinghai-Tibet Plateau, China.