Soil moisture is the primary factor limiting plant growth and vegetation rehabilitation in the loess region of northern Shaanxi, China. This 5-year (2008-2012) study investigated methods of selecting appropriate microsites for vegetation restoration based on efficient use of soil moisture; 5-year data were compared with 56 years of precipitation data using standardized precipitation index. In addition, the effects of microtopography on the spatiotemporal variations of soil moisture were analyzed at the Wuqi Ecological Station of Beijing Forestry University. Results showed that average annual precipitation during last 5 years fell by 12.4% during the growing season compared with 1957-2012 data and soil moisture content at depth of 0-160 cm under went dramatic changes and became relatively low in July and August. Soil moisture content varied in different microtopographical units as follows: gullies > gently-sloped terraces > collapsed soils > undisturbed slopes (control) > furrows > escarpments. The vertical distribution of soil moisture content in different microtopographical units showed dramatic changes at depth of 0-40 cm. Soil moisture content of gently-sloped terraces, gullies, collapsed areas, furrows, and undisturbed slopes was highest at depth of 80-160 cm with a level of instability at depth of 40-80 cm. For gently-sloped terraces and gullies, soil moisture content followed the order of 40-80 cm > 0-40 cm; for collapsed areas, furrows, and undisturbed slopes, soil moisture content follows the order of 0-40 cm > 40-80 cm. For escarpments, soil moisture content varied with depth in a different pattern: 0-40 cm > 80-160 cm > 40-80 cm. This study is of theoretical significance and will help guide the sustainable development of ecological restoration and vegetation rehabilitation in the Loess region.