Rodents, bats, and non-human primates are mammalian groups that share a significant proportion of microbes with humans. Comparing the contribution of these three mammalian taxa as reservoirs of zoonotic microbes and transmission hosts is important for preventing emerging infectious diseases in humans. In this study, we integrated data on host-microbe interactions of rodents (Rodentia), bats (Chiroptera), and non-human primates. We constructed host-microbe networks and microbe-sharing networks for both total microbes and human-associated microbes. We also compared the diversity of microbes of these three groups and their capacity for microbe transmission. The results suggested that non-human primates have a more significant role in the emergence and transmission of human-associated microbes compared to rodents and bats. Specifically, the average proportion of human-associated microbes carried per species of non-human primates was higher than that of the other two groups, demonstrating their greater capacity to carry these microbes. Furthermore, the microbe-sharing networks for non-human primates exhibited notably higher connectivity, suggesting that microbes may spread more easily among species within this group. In contrast, bats carry a high proportion of viruses among both their microbes and their human-associated microbes, underscoring their critical role in the emergence and transmission of human-associated viruses. Notably, the centrality of rodent species in the network surpassed that of both bats and non-human primates, indicating that the role of rodents in microbe transmission should not be underestimated. This study provides new insights into the significance of these three mammalian groups in the emergence and transmission of human-associated microbes, providing information for identifying potential hosts of emerging infectious diseases in humans.