Plateau zokor (Eospalax baileyi) is a native subterranean rodent living in alpine rangeland on the Qinghai–Tibet Plateau. The zokors excavate soil in their tunnels and push it out to form the zokor mound, which is secondary bare land on the ground. In the alpine rangeland ecosystem, the bare lands emit greenhouse gases and reduce carbon sequestration. However, little is known about the greenhouse gas emissions from the zokor mounds with bare soil. In this study, we used a gas analyzer in situ combined with a closed static chamber to monitor the emissions of CO₂ and CH₄ from new mounds, seminew mounds, old mounds, and the pasture without mounds. The biomass bacteria, fungi, and actinomycetes in the 0-to 20-cm soil layer of the mounds and the pasture without mounds were simultaneously investigated. To explore the source of the CO₂ and CH₄ emissions, we compared the differences of CO₂ and CH₄ flux in the zokors' active tunnels, tunnel-free soil, and mound-free pasture. The results showed that 1) the highest flux of CO₂ and CH₄ emissions in the same month was from new mounds, followed by seminew mounds, old mounds, and the pasture without mounds; 2) CO₂ and CH₄ emissions from the different mounds in 4 mo were significantly influenced by months and mound types, although there was no significant interaction between these factors; and 3) the flux of CO₂ and CH₄ emissions from the zokor mounds were significantly positively correlated with their total biomass of microbes and the flux of CO₂ and CH₄ inside the zokor active tunnels. The CO₂ and CH₄ inside the zokor active tunnels had more contributions to CO₂ and CH₄ emissions from the zokor mounds than the soil microbes' biomass in the mounds.