Climate change and human activities have increased the risk of soil erosion, resulting in widespread soil degradation in many regions worldwide. In this study, our purpose was to estimate the spatial and temporal changes in the integrated fertility indexes (IFI) of Northeast China from the 1990s to the 2010s from a regional perspective. The soil erosion modulus, calculated using the Revised Universal Soil Loss Equation, was combined with soil nutrient data for four nutrients in two time stages, and the response of soil fertility to soil erosion was analyzed under nine land-use patterns. The results indicated that soil fertility in Northeast China had decreased by 4.46% from the 1990s to the 2010s, with the IFI of cultivated land showing the smallest decline at 1.69%, followed by grassland at 4.81%, and forest land at 6.21%, in that order. The IFI of changed land-use decreased more than that of unchanged land-use. The △IFI (IFI in the 2010s minus IFI in the 1990s) was negatively correlated with the soil erosion modulus, particularly when the average soil erosion modulus exceeded 2 t/(ha/yr). Furthermore, △IFI was mostly negative, indicating obvious soil degradation. The contribution rate of nutrient loss in the 1990s averaged over 70%, which was significantly higher than that in the 2010s, indicating that non-point source pollution control and soil erosion interception measures implemented by most city governments after 2010 had been effective. In most cases, the contribution rates of the total potassium (TK) and soil organic carbon (SOC) in the 1990s were significantly higher than those of the other indicators, with the highest contribution rate of SOC loss being observed for cultivated land and the highest contribution rate of TK loss being observed for forest land and grasslands. Forest land is conducive to maintaining soil fertility, and when other types of land are converted into forest land, the contribution rate of nutrient loss decreases.