Soil moisture prediction is of great importance in crop yield forecasting and drought monitoring. In this study, the multi-layer root zone soil moisture (0-5, 0-10, 10-40 and 40-100 cm) prediction is conducted over an agriculture dominant basin, namely the Xiang River Basin, in southern China. The support vector machines (SVM) coupled with dual ensemble Kalman filter (EnKF) technique (SVM-EnKF) is compared with SVM for its potential capability to improve the efficiency of soil moisture prediction. Three remote sensing soil moisture products, namely SMAP, ASCAT and AMSR2, are evaluated for their performance in multi-layer soil moisture prediction with SVM and SVM-EnKF, respectively. Multiple cases are designed to investigate the performance of SVM, the effectiveness of coupling dual EnKF technique and the applicability of the remote sensing products in soil moisture prediction. The main results are as follows: (a) The efficiency of soil moisture prediction with SVM using meteorological variables as inputs is satisfactory for the surface layers (0-5 and 0-10 cm), while poor for the root zone layers (10-40 and 40-100 cm). Adding SMAP as input to SVM can improve its performance in soil moisture prediction, with more than 47% increase in the R-value and at least 11% reduction in RMSE for all layers. However, adding ASCAT or AMSR2 has no improvement for its performance. (b) Coupling dual EnKF can significantly improve the performance of SVM in the soil moisture prediction of both surface and the root zone layers. The increase in R-value is above 80%, while the reduction in BIAS and RMSE is respectively more than 90% and 63%. However, adding remote sensing soil moisture products as inputs can no further improve the performance of SVM-EnKF. (c) The SVM-EnKF can eliminate the influence of remote sensing soil moisture extreme values in soil moisture prediction, therefore, improve its accuracy.