Agricultural biodiversity have multiple functions. One of them is to control the occurrence and extent of pests and diseases. Biodiversity can be described as morphological, functional or interactional diversity. Comprehensive results can be determined by analyzing the diversity of interactional molecules. An effective strategy to promote crop growth and decrease pests’ development is to combine crop and non-crop species to benefit from the interaction of different species and varieties. Here we review advances in research and exploitation of agricultural biodiversity and we make further suggestion to build the structure and pattern of agricultural diversity based on the systemic research of the mechanisms underlying interactions between crops and organisms in agroecosystems. Those finding should be based on metagenomics, proteomics and metabolomics combined with physiology, biochemistry technology, monitoring and managing using ‘big data’ to achieve the green control for pest and sustainable development of agriculture.