As one of the world’s largest ecological rehabilitation programs, the three-north (Northern China, Northeastern China, and Northwestern China) shelterbelts program in China were not well evaluated on its effects on multiple soil properties. This paper aims to quantify this. Seven hundred twenty soils from paired plots of farmlands and neighbor shelterbelts were sampled from six regions of Songnen Plain in northeastern China. Multivariate analysis of variance and regression analysis were used to detect the impacts of shelterbelt plantations. For the overall 1 m soil profiles, shelterbelt plantations had a 4.3% and 7.4% decreases in soil bulk density and soil moisture (p = 0.000), a 4.8% increase in soil porosity (p = 0.003). It also evidently recovered soil fertility with a 40% increase in total P, a 4.4% increase in total K, and a 15.1% increase in available K (p < 0.05). However, without overall changes were in SOC and N (p > 0.05). Compared with farmland, shelterbelt plantations produced a 7.8% SOC increase in 20–40 cm soil and much more minor changes in surface soil (0–20 cm). Compared with the younger plantation, mature shelterbelts tended to sequestrate more SOC in soils (from a 0.11% decrease to a 3.31% increase) and recover total K from a 2.24% decline to a 16.5% increase. Correlation analysis manifested that there is a significant relationship between SOC sequestration and the changes in bulk density, porosity, soil moisture, pH, EC, total N, total P, and alkaline hydrolyzed N. In contrast, the strongest relationship was observed between total N and SOC (r > 0.50, p < 0.001). The increase in total N was accompanied by 1.01–1.67-fold higher SOC sequestration in deep soils >20 cm in poplar forests. Our results highlight that the over-40-year shelterbelts afforestation on farmland in northeastern China could strongly affect soil physics, soil water, and nutrient of P and K. The effects on SOC sequestration were dependent on soil depths, growth stages, and regions. Our data support the precise soil evaluation of agroforestry projects in the black soil region in the high-latitude northern hemisphere.