Accurate root zone soil moisture (RZSM) estimation is essential for precision irrigation (PI) systems that seek to optimize water use efficiency. Large-scale in-situ sensors for direct measurement are costly, while existing satellites lack depth resolution for direct RZSM data. Hence, in-direct RZSM estimation methods are required. Literature illustrates that RZSM at a location is related to changing soilwater-plant characteristics. Therefore, these characteristics can provide auxiliary information on RZSM changes. By leveraging auxiliary information derived from changing soil-water-plant characteristics, this paper enables indirect RZSM estimation at non-sensor locations, effectively addressing the limitations inherent in direct RZSM measurement techniques initially discussed. Compared to existing methods, deep learning (DL) is most suitable for such data associations as they are auto-tuned to extract relative relationships from diverse big data. Among DL models, sequential models are apt for finding these relationships as all these variables are time-series sequences. The transformer neural network (TNN) is the state-of-the-art DL model for analyzing sequences. However, for in-direct RZSM estimation, the data associations within a location and multiple sensor sites with the target need to be found. Conventional TNN cannot incorporate such simultaneous multi-associations, hence, we develop a new TNN model called the hybrid TNN model, which is able to facilitate the capturing of complicated dependencies through thoughtful feature selection and engineering. First, sensor locations exhibiting analogous downscaled 1-km satellite soil moisture (SM) are identified. Next, a dynamic multilayer perceptron (D-MLP) network discerns highly correlated auxiliary-RZSM data, utilizing both ground-based and downscaled satellite data. Following this, the dual attention module identifies essential multi-associations, leveraging selected sensor and target region information. Finally, the Bayesian layer averages multi-location RZSM using the conditional probability generated based on relative relationships to yield the target location RZSM estimate. Our proposed model shows 13.066% better RZSM estimation compared to popular sequential models. The hybrid TNN RZSM estimates are used to monitor root water depletion tolerance levels for optimal PI schedules, which shows 10.846% water and 10.339% cost-saving on our selected sites. Overall the proposed model effectively demonstrates that a more accurate PI predictive algorithm saves water, improves resource conservation, and reduces irrigation costs.INDEX TERMS Agriculture, deep learning, hybrid transformer neural network, precision irrigation, root zone soil moisture.