Targeting the Shawan natural regeneration ecosystem (converted from farmland in 2010) in Puding County, we adopted the eddy covariance (EC) system to carry out long-term positioning observations of carbon and water fluxes during the natural regeneration of ecosystems after farmland conversion in karst areas. Puding Station belongs to the National Field Scientific Observation and Research Network and the China Ecosystem Research Network. Based on the data processing requirements of the ChinaFLUX, we compiled in this dataset the carbon and water fluxes as well as conventional meteorological data in Shawan from 2015 to 2019, including net ecosystem carbon exchange (NEE), ecosystem respiration (Re), gross primary productivity (GPP), latent heat flux (LE), sensible heat flux (H), air temperature, air relative humidity, wind speed, wind direction, total solar radiation, net radiation, precipitation and so on. This dataset can provide observational evidence for the study of the carbon sink capacity and water consumption characteristics of the ecosystem at the early stage of natural regeneration after the conversion of sloping farmland to forest in karst areas in southern China, as well as their response to climate change.