Soil moisture (Mv) estimation and monitoring over agricultural areas using Synthetic Aperture Radar (SAR) are often affected by vegetation cover during the growing season. Volume scattering and vegetation attenuation can complicate the received SAR backscatter signal when microwave interacts with the vegetation canopy. To address the existing problems, this paper employed the model-based polarimetric decomposition method considering the two-way attenuation to remove the volume scattering and vegetation attenuation. A de-orientation process of SAR data was applied to remove the influence of randomly distributed target orientation angles before the polarimetric decomposition. To parameterize the two-way attenuation, Radar Vegetation Index (RVI) derived from the SAR intensity images was adopted. The Dubois model was used to describe backscattering from the underlying bare soil. Since the soil roughness parameters are difficult to measure under vegetation cover, the optimum surface roughness method was used to parameterize the Dubois model. This soil moisture retrieval algorithm was applied to the polarimetric multi-temporal RADARSAT-2 SAR data over soybean fields. The validation indicates the root-mean-square error of 9.2 vol.% and 8.2 vol.% at HH and VV polarization respectively over the entire soybean growing period, suggesting that the proposed method is capable of reducing the effect of vegetation cover for soil moisture monitoring over the soybean field.