In recent years, the burgeoning interest of enterprises in the e-commerce sector has underscored the necessity for effective analytical tools that monitor user engagement on agricultural products’ e-commerce platforms and provide precise market forecasts. To address this need, the current study proposes an analytical framework and develops a comprehensive market prediction system for agricultural products. Initially, behavioral analysis indices on the e-commerce platform are employed to delineate user behavioral patterns, which include traffic and purchase path analyses. Based on a case study, enhancements are made to the conventional RFM (Recency, Frequency, Monetary) customer behavior model, both strategically and structurally, thus enriching the analysis of user behavior on such platforms. Subsequently, a four-tiered e-commerce market prediction system is established, incorporating a multilayered deep learning network designed to anticipate market trend shifts. The analysis reveals that the application of deviation standardization processing significantly refines the representation of user behavior to the platform’s merchants. Moreover, the implementation of this market prediction system not only reduces processing time from 8 seconds to 4 seconds but also decreases the average relative error by 0.31%. These improvements highlight the system’s enhanced predictive accuracy, confirming its utility in navigating the complexities of the agricultural products market in the e-commerce domain.