Deforestation for agricultural development or extension is a common land-use problem that may cause a series of changes in the ecological environment and soil carbon stock in planting systems. However, the response of soil physical, chemical properties and carbon stocks in agricultural systems in the initial period after deforestation have not been thoroughly examined, especially in the subsoil. We investigated the variations in the soil physicochemical properties and organic carbon stocks to a depth of 100 cm in a poplar (Populus deltoides cv. 35) plantation, a summer maize (Zea mays L.) followed by winter wheat (Triticum aestivum L.) field after 1 year of deforestation of a poplar plantation, and a wheat–maize rotation field used for decades. The soil bulk density and pH decreased, and the soil total nitrogen (TN), total phosphorus, and total potassium contents increased considerably. The soil organic carbon (SOC) content and stocks (to 100 cm) increased by 32.8% and 20.1%, respectively. The soil TN content was significantly (p < 0.001) positively correlated with the SOC content, and the C:N ratio increased for the field following deforestation. Furthermore, the nitrogen in the poplar plantation and the field following deforestation was limited. We recommend increasing the amount of nitrogen fertilizer following deforestation to improve fertility and this will be beneficial to SOC storage.