An accurate analysis of nutrient balance in different cropping systems is necessary for improving soil fertilities, causing higher crop yields and quality. This study was carried out to investigate the nutrient balance, changes in soil properties, and their effects on crop yield in long-term field cultivation under mono- and rotation-cropping systems (MCS and RCS, respectively). The analytical results of the soil properties showed that the application of mineral fertilizers alone in the MCS leads the reduction of soil CEC, exchangeable Ca, and microbial biomass C and N. Compared with the MCS of soybean, the RCS of soybean and barley significantly improved the soil properties, which increased crop yield. It might be due to the barley residue added to the RCS soil. Mean nutrient balances for 4 years were -55.9 kg N, +34.7 kg $P_2O_5$, and -0.3 kg $K_2O$ $ha^{-1}$ for the MCS and +19.7 kg N, +107.4 kg $P_2O_5$, and -48.6 kg $K_2O$ $ha^{-1}$ for the RCS, respectively. These nutrient imbalances mean that conventional fertilizer recommendations were inadequate for maintaining soil nutrient balance. From these results, we can conclude that the crop rotation may change comprehensive physical, chemical, and biological soil properties. These changes could affect the nutrient balance and then the crop yield.