The population of the plateau zokor (Myospalax fontanierii) rapidly increases on the degraded alpine meadows of Qinghai–Tibetan Plateau. The burrowing and feeding activities of plateau zokor exert huge effects on the plant community and soil properties. However, the possible effects on the production and consumption of greenhouse gases have not been investigated. To evaluate the effects, we measured the ecosystem respiration (Re), soil methane (CH 4 ) and nitrous oxide (N 2 O) fluxes and the main soil, vegetation and environmental factors of zokor mounds of different excavation years (one-, two- and three to five-year, hereafter referred to as ZM1, ZM2 and ZM3–5) and surrounding control meadow (CM) in a typical Kobresia humilis meadow from July to November 2012. The cumulative Re, CH 4 uptake and N 2 O emissions were 1.82 ± 0.28, 2.83 ± 0.48, 3.13 ± 0.13 and 3.91 ± 0.27 ton C ha −1 , 1.55 ± 0.27, 1.33 ± 0.15, 1.20 ± 0.16 and 1.02 ± 0.25 kg C ha −1 and 0.23 ± 0.02, 0.10 ± 0.04, 0.08 ± 0.01 and 0.07 ± 0.02 kg N ha −1 for ZM1, ZM2, ZM3–5 and CM, respectively. The soil CH 4 uptake and N 2 O emission were stimulated and the Re was inhibited for ZM1, ZM2 and ZM3–5 as compared to the CM. If the distribution area of zokor mounds increased from 2% to 6%, the combined CO 2 -equivalent of CH 4 and N 2 O exchanges strengthened 3.2 times. Furthermore, the composition of plant community altered; the plant biomass, topsoil organic carbon content, temperature and moisture decreased; and the topsoil gas permeability, inorganic nitrogen and dissolved organic carbon contents increased on zokor mounds as compared to the CM (P < 0.05). The recovery process of the vegetation and soil organic carbon pools of zokor mounds requires many years (>10 years). In view of the loss of soil organic carbon and the stimulation of N 2 O emission, the increasing distribution area of zokor mounds weaken the function of alpine meadows on the Qinghai–Tibetan Plateau as a greenhouse gas sink.