Deep-rooted plants have increasingly been introduced after cropland abandonment with the implementation of the ‘Grain-for-Green’ program on the Chinese Loess Plateau (CLP). However, the temporal patterns of soil moisture content (SMC) and soil organic carbon (SOC) with stand ages and the potential role of deep roots driving these patterns within deep profiles are still poorly understood. Here, we investigated variations in fine root distribution, SMC, and SOC content and density in 0–500 cm soil profiles under two deep-rooted plant systems with different stand ages (black locust plantation, Robinia pseudoacacia L.; and apple orchard, Malus pumila Mill.), evaluated their soil moisture deficit (SMD) and SOC sequestration effect relative to cropland, and attempted to characterize the role of deep roots in driving these variations. The results confirmed severe SMD in all soil layers within the 0–500 cm profile under black locust plantations, relative to cropland, but noting some SMC recovery under the 38-year-old black locust plantation. In contrast, depth-averaged (0–500 cm) SMC increased notably during the initial 5 years and then declined continuously over time under apple orchards. These results suggest the temporal pattern of SMC varies with deep-rooted systems. The SOC density of the 100–500 cm layer accounted for more than half of the entire profile, and SOC accumulation mostly occurred at depths below 300 cm under the two deep-rooted systems, which indicates the great importance of deep soils for carbon sequestration. The temporal patterns of deep SOC were different from those in surface soils. Obvious carbon losses were detected within the 20–500 cm soil profile under the 38-year-old black locust plantation. The linkages between SMC and SOC content were typically stronger under black locust plantations than under apple orchards. The influence of roots on SMC was stronger under apple orchards than under black locust plantations. Suitable land management practices are recommended to restore the fragile ecosystem of the CLP. Overall, our findings provide new insights for sustainable vegetation restoration in restored ecosystems.