Plateau pikas ( Ochotona curzoniae ) disturbance and patchiness intensify the spatial heterogeneous distribution of vegetation productivity and soil physicochemical properties, which may alter ecosystem carbon emission process. Nevertheless, previous researches have mostly focused on the homogeneous vegetation patches rather than heterogeneous underlying surface. Thus, this study aims to improve our understanding of the difference in ecosystem respiration (Re) over heterogeneous underlying surface at the plot scale in an alpine meadow grassland. Six different land surface: large bald patch, medium bald patch, small bald patch, intact grassland, above pika tunnel and pika pile were selected to analyze the response of Re to pikas disturbance and patchiness, and the key controlling factors. The results showed that (1) soil moisture (SM) under pika pile and bald patches was 2–11 % less than intact grassland despite pikas disturbance increased water infiltration rate, while soil temperature (ST) under pika pile and bald patches was 1–3 ℃ higher than intact grassland; (2) soil organic carbon (SOC) and total nitrogen (TN) density under above pika tunnel were 2.45–3.31 and 2.10–3.72 times higher than other surface types; and (3) Re under intact grassland and above pika tunnel were 0.22–1.07 times higher than pika pile and bald patches, and Re was significantly correlated with SM, TN and vegetation biomass (P < 0.05). Our results suggested that pikas disturbance and patchiness altered ecosystem carbon emission pattern, which was mainly attributed to the reduction of soil water and supply of substrates. Given that the wide distribution of pikas and large area of bald patches, the varied Re under heterogeneous underlying surfaces should not be neglected for estimation of ecosystem carbon emission at plot or region scale.