By integrating the thermal characteristics from thermal-infrared remote sensing with the physiological and structural information of vegetation revealed by multispectral remote sensing, a more comprehensive assessment of the crop soil-moisture-status response can be achieved. In this study, multispectral and thermal-infrared remote-sensing data, along with soil-moisture-content (SMC) samples (0~20 cm, 20~40 cm, and 40~60 cm soil layers), were collected during the flowering stage of soybean. Data sources included vegetation indices, texture features, texture indices, and thermal-infrared vegetation indices. Spectral parameters with a significant correlation level (p < 0.01) were selected and input into the model as single- and fuse-input variables. Three machine learning methods, eXtreme Gradient Boosting (XGBoost), Random Forest (RF), and Genetic Algorithm-optimized Backpropagation Neural Network (GA-BP), were utilized to construct prediction models for soybean SMC based on the fusion of UAV multispectral and thermal-infrared remote-sensing information. The results indicated that among the single-input variables, the vegetation indices (VIs) derived from multispectral sensors had the optimal accuracy for monitoring SMC in different soil layers under soybean cultivation. The prediction accuracy was the lowest when using single-texture information, while the combination of texture feature values into new texture indices significantly improved the performance of estimating SMC. The fusion of vegetation indices (VIs), texture indices (TIs), and thermal-infrared vegetation indices (TVIs) provided a better prediction of soybean SMC. The optimal prediction model for SMC in different soil layers under soybean cultivation was constructed based on the input combination of VIs + TIs + TVIs, and XGBoost was identified as the preferred method for soybean SMC monitoring and modeling, with its R2 = 0.780, RMSE = 0.437%, and MRE = 1.667% in predicting 0~20 cm SMC. In summary, the fusion of UAV multispectral and thermal-infrared remote-sensing information has good application value in predicting SMC in different soil layers under soybean cultivation. This study can provide technical support for precise management of soybean soil moisture status using the UAV platform.