The current agricultural production model in China is transitioning from traditional to smart agriculture. In response to the continuous expansion of data scale in various agricultural organizations and the problem of "Data Silos" in data sharing, it is difficult to gather agricultural data on a large scale to guide precise agricultural decision-making. This study is based on Cloud-Blockchain Integration and data security governance related technologies in distributed agriculture scenarios to solve the above-mentioned problems and explore their practical application effects. In a distributed agricultural scenario, based on IPFS, blockchain, and cloud computing, design an agricultural big data governance algorithm that can be deployed on smart contracts, construct a multi-party agricultural data aggregation model, as well as a complete, secure, traceable data protection model and typical scenario application model. Taking the agricultural production of Huaxing Farm and its affiliated agricultural organizations in Changji, Xinjiang as an example, further build a Cloud-Blockchain Integration agricultural big data platform. By comparing the performance of the agricultural big data governance model based on Cloud-Blockchain Integration with two traditional models, the experiment shows that the comprehensive performance of the model in this article can achieve a better balance and achieved better performance compared to the traditional models.