Analysis and application about large data of crop Breeding, was not pure was a kind of technology evolution, but changed to mining and analysis large data of crop breeding use multiple granularity, multi-level and multi-channel analysis model and tools. According to the existing situation, this paper from the perspective of data integration, tool integration, method integration, put forward an model, it definition and description data and tools in the process analysis and application about large data of crop breeding, and then, set up a basic agent model frame structure, reasonably and effectively integrate all kinds of data and tools, so as to realize intelligent coordination, reasonable scheduling, the purpose of further improve the joint study, analysis mining.