A dataset of biological indicators in paddy fields at the Qianyanzhou Station (2003–2021)

China faces multiple challenges, including constraints on arable land resources, ecological pressures, and the demand for food security. Particularly, the red soil hilly regions of southern China support 27.8% of the nation′s cultivated land, but these regions face soil acidification, nutrient depletion, and ecological fragility. The coexistence of seasonal drought and high-intensity land use makes long-term observational data especially valuable. Long-term fixed-site experiments in farmland ecosystems, through continuous and systematic data collection, can reveal the evolutionary patterns of agricultural ecosystems and provide critical evidence for optimizing sustainable management strategies. This dataset is based on long-term fixed-site observations (2003–2021) from the Jiangxi Qianyanzhou Critical Zone Observatory of Red Soil Hilly Region, a National Field Scientific Observation and Research Station. It focuses on a typical double-cropping rice system in the red soil hilly region, systematically recording biological parameters such as crop yield, growth period dynamics, harvest traits, leaf area index (LAI), plant nutrient content, and fertilization data under different nutrient management practices. Data acquisition and subsequent processing strictly adhere to the standardized operational system established by CERN. Covering 19 years, the dataset includes comparisons of three farming practices: conventional fertilization, straw return, and a control group without fertilization. It comprehensively presents the productivity responses and nutrient cycling characteristics of farmland ecosystems in the red soil hilly regions of southern China. This dataset not only provides foundational data support for agronomy, ecology, and soil science research but also offers a scientific basis for improving cultivated land quality and synergistically enhancing productivity in red soil regions. It is of significant importance for ensuring national food security and promoting sustainable agricultural development.