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In order to improve the effect of agricultural economic structure optimisation, this paper builds an agricultural economic structure optimisation analysis system based on factor analysis and intelligent algorithms, and uses a set of low-dimensional hidden factor vectors to describe the covariance matrix structure of high-dimensional observation vectors. Moreover, this paper combines the algorithm with the actual situation to obtain the optimisation analysis process of the agricultural economic structure. On this basis, this paper analyses the optimisation of agricultural economic structure in practice with a case analysis method. Moreover, this paper uses mathematical analysis to process agricultural economic structure data, and uses mathematical statistics to visualise the process of data processing. In addition, this paper combines the weighted average to perform parameter processing, combines with the comparative analysis method to obtain the agricultural economic results parameters, and analyses these parameters. Finally, on the basis of the above, this paper proposes the corresponding optimisation strategy of agricultural economic structure. The research results show that the method proposed in this paper has a certain effect. [ABSTRACT FROM AUTHOR]