The increasing serious droughts recently might have significant impacts on socioeconomic development in the Red River basin (RRB). This study applied the variable infiltration capacity (VIC) model to investigate spatio-temporal dynamics of soil moisture in the northeast, northwest, and Red River Delta (RRD) regions of the RRB part belongs to territory of Vietnam. The soil moisture dataset simulated for 10 years (2005–2014) was utilized to establish the soil moisture anomaly percentage index (SMAPI) for assessing intensity of agricultural drought. Soil moisture appeared to co-vary with precipitation, air temperature, evapotranspiration, and various features of land cover, topography, and soil type in three regions of the RRB. SMAPI analysis revealed that more areas in the northeast experienced severe droughts compared to those in other regions, especially in the dry season and transitional months. Meanwhile, the northwest mainly suffered from mild drought and a slightly wet condition during the dry season. Different from that, the RRD mainly had moderately to very wet conditions throughout the year. The areas of both agricultural and forested lands associated with severe drought in the dry season were larger than those in the wet season. Generally, VIC-based soil moisture approach offered a feasible solution for improving soil moisture and agricultural drought monitoring capabilities at the regional scale.