Objective The objectives of this study were to establish a spatial reconstruction framework for soil profiles applicable to small-sample conditions and to quantitatively characterize the spatiotemporal differentiation of key soil properties and their driving factors in cropland profiles in Nenjiang from 1980 to 2023.

Methods Thirty paired representative soil profiles collected in 1980 and 2023 in Nenjiang were analyzed. By integrating multi-source environmental covariates, an innovative small-sample hierarchical spatial reconstruction modeling framework was developed. Non-parametric ANOVA was employed to quantify the spatiotemporal evolution of key soil properties, while redundancy analysis (RDA) was used to identify the dominant environmental drivers of profile-scale soil changes.

Results ① The proposed small-sample reconstruction framework proved robust and effective, with regression kriging (RK) identified as the optimal model. ② Profile-scale analysis revealed pronounced subsurface degradation. Total nitrogen (TN) exhibited severe depletion across the entire profile (−36.43%), total phosphorus (TP) deficiency was concentrated in the mid- to lower layers (30–80 cm) without fertilizer supplementation, whereas total potassium (TK) showed general enrichment throughout the profile, indicating an increasing nutrient imbalance. Degradation patterns also differed among soil types. Chernozems displayed a "sharp nutrient loss but stable horizon thickness" characteristic of hidden degradation, while Meadow soils primarily experienced physical degradation due to drainage-induced subsidence. ③ The driving mechanisms of soil property changes exhibited distinct vertical differentiation. Variations in the 0–30 cm layer were mainly controlled by anthropogenic disturbance and hydrological processes, whereas those in the 30–80 cm layer were governed primarily by topography- and hydrology-related natural factors.

Conclusion This study established and validated an effective approach for spatiotemporal reconstruction and attribution analysis of key soil profile indicators under small-sample conditions. The findings demonstrated that the degradation of Nenjiang’s black soils was a systemic process extending throughout the soil profile. The identified vertical differentiation of driving factors provided essential scientific evidence and data support for depth-specific and stratified conservation and nutrient management strategies in black soil region of Northeast China.