Compared with other terrestrial natural ecosystems, the land-atmosphere interaction in managed farmland ecosystem is more complex and changeable, due to the effect of crop types, cropping pattern, management practices, etc. As one of the most effective measures against the process of land alkalization and salinization in the Songnen Plain of Northeast China, paddy rice planting after desalination highly representative model for studying climate mitigation, water use and carbon balance. To support this approach effectively, it requires comprehensive field monitoring data. The eddy covariance method, grounded in micrometeorological theory, is widely recognized as the primary and direct approach for measuring CO2 and H2O exchanges in farmland ecosystems. This dataset comprises field measurements of Changling alkali-saline paddy rice during 2018–2020 subjected to rigorous quality control and gap filling in accordance with the ChinaFLUX data processing criteria. The dataset specifically includes half-hourly, daily, monthly and yearly scales of air temperature (Ta), air relative humidity (RH), water vapor pressure (e), saturated water vapor pressure (es), soil temperature (Ts), soil water content (SWC), net radiation (Rn) with four components, photosynthetically active radiation (PAR), rainfall (P), wind speed (Ws), wind direction (Wd), sensible heat flux (Hs), latent heat flux (LE), evapotranspiration (ET), net ecosystem CO2 exchange (NEE), ecosystem respiration (Re), gross ecosystem exchange (GEE), etc. The establishment and sharing of this dataset can offer valuable data support and a solid theoretical foundation for regional farmland ecosystem assessment and management.