The presence of burrowing mammals can have extensive effects on plants and soils, creating bare soil patches in alpine meadows and potentially altering plant-soil carbon (C) and nitrogen (N). This study focuses on the plateau pika (Ochotona curzoniae) to examine the responses of plant-soil C and N to a small burrowing mammal from quadrat scale to plot scale. The density of active burrow entrances in disturbed plots was used as an indicator of the disturbance intensity of plateau pikas. The study found that the below-ground biomass (BGB) and its C and N, as well as soil C and N concentrations were significantly lower in bare soil areas than in vegetated areas and undisturbed plots. This shows that the quadrat scale limited the estimation of the C and N sequestration potential. Therefore, further research on the plot scale found that the disturbance by plateau pika significantly reduced plant biomass and BGB carbon stock. However, plateau pika did not affect soil C and N stocks or ecosystem C and N stocks. These findings suggest the bare soil patches formed by plateau pika caused plant and soil heterogeneity but had a trade-off effect on plant-soil C and N stocks at the plot scale. Nevertheless, moderate disturbance intensity increased the C and N sequestration potential in grassland ecosystems. These results provide a possible way to estimate how disturbance by small burrowing mammals affects C and N cycling in grassland ecosystems while accurately assessing the effects of small burrowing mammal densities on C and N in grassland ecosystems.