Extensive areas of agricultural land have been abandoned to ecological restoration in recent years in the karst region of Southwest China, which contributes to the greening of the area. However, there has yet no direct observation of carbon, water, and energy fluxes on abandoned land in the region. In addition, because of the coupling between above and below-ground processes, monitoring of the karst ecosystem needs to be conducted from a critical zone perspective. In this study, an integrated vertical observation system through air-vegetation-soil-cave continuums was constructed on abandoned farmland under natural restoration in Puding Karst Ecosystem Research Station. Preliminary results show that: First, vegetation cover restored rapidly after abandonment, and the measured net ecosystem exchange (NEE), soil CO2 efflux, actual evapotranspiration (ETa) and latent heat (LE) in the rainy season are about twice of that in the dry season, this strong seasonal variation relates to the typical subtropical monsoon climate with synchronous water and heat availability during rainy season. Second, high CO2 concentrations and significant CO2 variation in the monitored cave indicate that the exchange of underground carbon pools with the atmosphere cannot be neglected in the carbon budget of the study site.