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Previous studies have proved that root distribution along gully headwalls greatly alters soil properties and further affects the soil erodibility of gully heads. However, it is not clear whether the gully headcut migration is affected by root distribution and soil properties. Five representative gullies developed in different land uses were selected to clarify the variations of root distribution and soil properties and their effects on headcut migration in the rainy season (May to October 2021) in the Mollisols region of northeast China. Results showed that the 68.4%–93.3% of root mass density and 65.6–88.5% of root length density were concentrated in 0–30 cm soil layer of gully heads, and the roots of 85%. The gullies developed in farmlands had relatively higher soil compactness, shear strength and aggregate stability, but lower organic matter (OMC), disintegration capacity and soil permeability than those developed in woodlands, unpaved roads in farmland and stable gully-beds. Changes in soil properties of gully heads were closely related to root density. The linear, areal, and volumetric migration rate of gully heads varied greatly and were 1.07–35.11 m yr−1, 28.95–562.46 m2 yr−1 and 56.82–6626.37 m3 yr−1, respectively, with the average of 9.07 m yr−1, 156.92 m2 yr−1 and 1503.02 m3 yr−1, respectively. The change in headcut migration rate was significantly affected by root density, soil properties and drainage area, of which soil texture, OMC, soil aggregate structure, and the drainage area were the critical factors influencing headcut migration in the Mollisols region of northeast China.