Using the eddy covariance flux observation technique based on micrometeorology theory, we directly measured the functions and processes of the productivity, energy partitioning and water use of natural oak forest ecosystems at a transitional area between subtropical and warm temperate zones, which can provide an important data basis for studying the mechanism of carbon and water cycle in forest ecosystems. This study focused on a natural oak forest located at the Baotianman Ecological Research Station. We employed a combination of the eddy covariance system and an environmental gradient system for long-term and continuous observations, and we further organized, quality-controlled, and analyzed the monitoring data collected from January 2017 to December 2018. The dataset includes various data variables, such as air temperature and humidity, soil temperature and humidity, wind speed, wind direction, photosynthetically active radiation, upward/downward shortwave radiation, upward/downward longwave radiation, net radiation, sensible heat flux, latent heat flux and carbon flux. The dataset is composed of the observation data on half-hourly, daily monthly, and yearly scales. It is expected to provide a database for studying the response and adaption mechanisms of typical forest ecosystems to climate change in transitional areas between subtropical and warm temperate zones.