Land use change has significant influences on many biogeochemical and ecological processes in peri-urban ecosystems, especially for soil carbon and nitrogen cycles. Identifying the relationship between land use change and soil processes in peri-urban areas is a key issue in current studies. In this study, the Zhangxi watershed was selected as the study area, which is a typical peri-urban watershed in the Yangtze River Delta. The land use changes were analyzed from 1974 to 2015 based on remote sensing images. The DNDC (DeNitrification-DeComposition) model was used to simulate soil organic carbon and soil total nitrogen changes in this period. The results showed that from 1974 to 2015, area of forestland and farmland decreased because of urbanization, and the area of urban construction land increased. Calibration of the DNDC model showed that the simulated values were consistent with observed values. This indicated that the calibrated DNDC model can accurately simulate soil organic carbon and soil total nitrogen in the study area. Results of the DNDC model showed that soil organic carbon and soil total nitrogen content per unit area in farmland decreased during the simulation period, and the content decreased with increasing temperature and the amount of precipitation. The values of soil organic carbon and soil total nitrogen content per unit area in orchards displayed no obvious changes during the past 41 years, and soil organic carbon and soil total nitrogen in orchards were sensitive to temperature changes. The soil organic carbon and total nitrogen per unit area in forestland increased during the simulation period and increased with increasing temperature and decreased with increasing amounts of precipitation. At the watershed scale, simulation results showed that the total amount of soil organic carbon and soil total nitrogen in farmland decreased from 1974 to 2015, and the values in orchard increased. The soil organic carbon in forestland increased during simulated years, whereas the soil total nitrogen decreased in early simulated years and increased in the recent two decades. The changes in total organic carbon and total nitrogen reserves at the watershed scale were dominated by forestland because of the high content of soil organic carbon and total nitrogen in forestland and its large area in the watershed. This indicated that land use type and its composition determines the characteristics of soil organic carbon and total nitrogen storages at the watershed scale. This study showed that both land use, and climate factors (temperature and precipitation) have effects on soil organic carbon and soil nitrogen storage, and land use take a determining role in this process. Results of this study could provide scientific guidance on soil security and land use optimization in rapid urbanization areas.