Soil moisture is crucial to vegetation restoration in karst areas, and climate factors and vegetation restoration are key factors affecting changes in soil moisture. However, there is still much controversy over the long-term changes in soil moisture during vegetation restoration. In order to reveal the changes in soil moisture during vegetation restoration, we conducted long-term positioning monitoring of soil moisture at 0–10 and 10–20 cm on secondary forests sample plot (SF, tree land) and shrubs sample plot (SH, shrub land) in karst areas from 2013 to 2020. The results showed that the aboveground biomass of SF and SH increased by 50% and 240%, respectively, and the soil moisture of the SF and SH showed an increasing trend. When shrubs are restored to trees in karst areas, the soil moisture becomes more stable. However, the correlation coefficients (R²) between the annual rainfall and the annual average soil moisture of SF and SH are 0.84 and 0.55, respectively, indicating that soil moistures in tree land are more affected by rainfall. The soil moisture of shrubs and trees are relatively low during the months of alternating rainy and dry seasons. Rainfall has a very significant impact on the soil moisture of tree land, while air temperature and wind speed have a significant impact on the soil moisture of tree land, but the soil moistures of shrub land are very significantly affected by rainfall and relative humidity. Therefore, during the process of vegetation restoration from shrubs to trees, the main meteorological factors that affect soil moisture changes will change. The results are important for understanding the hydrological processes in the ecological restoration process of different vegetation types in karst areas.