Nature-based biodiversity agriculture is currently recognized as the best path for green agriculture. Agricultural systems with biodiversity can provide ecological functions such as pest and greenhouse gas emission control, water and nutrient regulation, pollination, etc. How to construct a healthy agricultural biodiversity system and make it play a beneficial role for green agriculture is an urgent issue that needs attention. Thus, this study summarizes traditional biodiversity utilization and cultivation techniques and their comprehensive effects. Results showed that paddy rotation modes improved rice yield and enhanced soil fertility indicators such as soil organic matter (SOC), total nitrogen (TN), available phosphorus (AP), and available potassium (AK). Paddy co-culture modes effectively suppressed major pests and diseases, including rice planthopper, rice leaf roller, rice blast, and weeds, with reductions ranging from 15.5 % to 73.9 %. Organic fertilization and straw returning practices increased microbial diversity, as evidenced by the rise in bacterial (1.9 %–7.5 %) and fungal (6.5 %–24.1 %) Shannon index. Based on these findings, this study identifies three key challenges in promoting agricultural biodiversity in modern intensive farming: efficiency in human resource utilization, integration of functions, and adaptation to environmental heterogeneity. And then proposed the “four zones” strategies including production functional zone, production and ecological service combined functional zone, production service and ecological service combined functional zone, and ecological service functional zone. As a conclusion, the study highlights that the rational spatial configuration and species combination of these zones under diverse climatic and land-use conditions is essential for achieving the dual goals of ecological sustainability and economic viability, and should be a key focus for future research and practice.
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