CH₄ serves as an important greenhouse gas, yet limited knowledge is available in global and regional CH₄ cycling, particularly in widely distributed karst terrain. In this study, we investigated an upland in Puding Karst Ecosystem Research Station, and explored CH₄ concentration and/or flux in atmosphere, soil and cave using a closed static chamber method and an eddy covariance system. Meanwhile, we monitored atmospheric temperature, precipitation, temperature and wind velocity in the cave entrance. The results demonstrated that atmospheric CH₄ and actual soil CH₄ fluxes in the source area of eddy covariance system were −0.19 ± 8.64 nmols⁻¹m⁻² and -0.16 nmols⁻¹m⁻² respectively. The CH₄ concentrations in Shawan Cave exhibited 10 ∼ 100-fold lower than that of the external atmosphere. CH₄ oxidation rate dominated by methane-oxidizing bacteria was 1.98 nmols⁻¹m⁻² in Shawan Cave when it combined with temperature difference between cave and external atmosphere. Therefore, CH₄ sink in global karst subterranean spaces was estimated at 106.2 Tg CH₄ yr⁻¹. We supplemented an understanding of CH₄ cycling paths and fluxes in karst terrain, as well as CH₄ sinks in karst subterranean space. Further works require to establish a karst ecosystem observation network to conduct long-term integrated studies on CH₄ fluxes regarding atmosphere, soils, plants and caves.