Large gullies occur globally and can be classified into four main micro-topographic types: ridges, plane surfaces, pipes and cliffs. Afforestation is an effective method of controlling land degradation worldwide. However, the combined effects of afforestation and micro-topography on the variability of soil moisture remain poorly understood. The primary objectives of this study were to determine whether afforestation affects the spatial pattern of the root-zone (0–100 cm) soil moisture and whether soil moisture dynamics differ among the micro-topographic types in gully areas of the Chinese Loess Plateau. The results showed that in the woodland regions, the spatial mean moisture values decreased by an average of 6.2% and the spatial variability increased, as indicated by the standard deviation (17.1%) and the coefficient of variation (22.2%). In general, different micro-topographic types exerted different influences on soil moisture behavior. The plane surface presented the largest average soil moisture values and the smallest spatial variability. The lowest soil moisture values were observed in the ridge, mainly due to the rapid drainage of these areas. Although pipe woodland region can concentrate surface runoff during and after rainfall, the larger trees growing in these areas can lead to increased soil moisture evapotranspiration.