Anthropogenic activities have altered the global nitrogen (N) cycle, leading to increased N input into the ecosystem through N deposition and N fertilizer. China consumes the highest amount of fertilizer globally, and it has become the third largest N deposition region in the world. N input is an important factor in the terrestrial carbon (C) sink, and N input is implicated in a series of biogeochemical cycles that then influence the C cycle and its spatial pattern. The soil C pool plays an important role in the global C cycle; therefore, the question of whether and to what extent N input affects the soil C pool must be addressed in relation to global change and N deposition. Northeast China has the third-largest black belt in the world and it is an important commodity grain base of China. Cropland is the most prominent manner of land use in the Northeast, and the change in its soil C pool is an essential factor in explaining the regional C budget and maintaining soil fertility. Using a process-based carbon-water-nitrogen coupling model, CEVSA2, we simulated the spatial patterns of N deposition in China between 1961 and 2010. With the N deposition and environment data collected, we also used CEVSA2 to explore the effect of enhanced N input on soil C storage in Northeast China in this period. The results show that the N deposition in Northeast China (1.00 gN m^-2 a^-1) is higher than the average for the whole country, and increases annually by 0.047 gN m^-2 a^-1. From the 1980, the N input began to increase significantly. The model simulations indicated that enhanced N deposition has resulted in a net increase of soil C density by 135 gC/m² in Northeast, and the total soil C storage increased by 0.16 PgC over the past 50 years. The soil C sequestration induced by N input decreased from east to west and from south to north. In the Songliao Plain and the Sanjiang Plain, the soil C sequestration induced by N input was >300 gC/m². The change in soil C density induced by N input varies significantly among the major biome types in the Northeast. Model simulations indicated that the increase in soil C density in cropland was 230 gC/m². However, those in the forest, shrubland, and grassland were 76 gC/m², 169 gC/m² and 89 gC/m², respectively, and the spatial heterogeneity of N input as well as the different responses of vegetation types to it determined the spatial pattern of the increase in soil C storage. Elucidation of the effect of N input on soil C storage will provide a scientific foundation for C fixation as well as C and N management in cropland.