Black soil in northeastern China has suffered widespread soil degradation due to long-term cultivation while causing eroded–depositional landscapes, leading to soil-associated carbon redistribution. In agricultural systems, adding exogenous organic material to degraded soil is a common measure to improve soil aggregate stability and soil quality. However, differences in soil properties may alter the decomposition and turnover of organic material in aggregates. Using a uniform method to restore the eroded (E) and depositional (D) soils is inefficient. Therefore, an indoor constant temperature and humidity incubation experiment with the addition of three organic materials, namely, straw (S), biochar (B), and swine manure (M), was designed with an equal amount of carbon. Soil aggregate composition, stability, and organic carbon from eroded and depositional soils were analyzed for evaluating the amendment efficiency of soil quality by exogenous organic material addition. The main results were as follows: adding straw and swine manure could effectively promote >2-mm aggregates formation (E: 7.1%, 8.8%; D: 17.3%, 8.6%) and significantly improved the mean weight diameter (MWD) (E: 0.45 mm, 0.52 mm; D: 0.96 mm, 0.54 mm), while the addition of biochar significantly increased the proportion of 0.25–2-mm aggregates (E: 7.9%; D: 10.9%), but the effect of improving MWD was less than straw and swine manure. All the three organic materials could significantly increase soil total organic carbon (TOC) (S, B and M: 1.95, 3.12 and 2.46 g·kg−1) in the eroded area, and the effect of biochar was the best, whereas it was not significant for the soil in the depositional area. Specially, adding swine manure and adding straw is more beneficial to the restoration of eroded areas and depositional areas, respectively.