Alfalfa (Medicago sativa L.) is a primary and widely cultivated forage crop in China. As a perennial leguminous grass, continuous planted alfalfa may influence carbon and nitrogen sequestration in soils. We evaluated the effect of alfalfa, planted for different lengths of time, and temperature and precipitation on soil organic carbon (SOC) and total nitrogen (TN) contents, and estimated soil SOC and TN inventories from 0-60 cm in three agro-pastoral ecotones of northern China. Alfalfa SOC and TN storage patterns were significantly different with increasing soil depths between the three regions of northern China. Continuous alfalfa grassland planted had a positive effect on accumulation of both SOC and TN in the Northwest region, whereas SOC storage peaked 6-7 years after planting in the Northeast and North region. Moreover, relatively higher TN storage appeared 7 years after planting in the Northeast and North regions. This study controlled as many factors as possible, but we caution that such temporal inferences could be artifacts of site selection. The regression analysis indicated that SOC and TN accumulation was mainly dependent on temperature (≥10°C of effective total accumulated temperature) in the North region. Precipitation in the growing season was the main limiting factor for SOC storage in the Northwest region and TN accumulation in the North regions. Therefore, the different climate factors affecting SOC and TN sequestration in alfalfa occurred at a regional scale.