Soil quality (SQ), a measure of the sustainability of land use and soil management practices, can be assessed by indicators including soil physical, chemical, and biological properties. Our primary objectives were to investigate the influence of consecutive cultivation and different crop rotation systems on individual SQ indicators and to examine the impact of rotation systems on SQ using soil quality index (SQI) model. A site-specific selection of 17 potential SQ indicators representing soil chemical and physical attributes (0-10 cm) and groundwater features on 60 sampling locations and 10 representative soil profiles was chosen in a typical coastal newly reclaimed farmland of north Jiangsu Province, China. Using ANOVA analysis, the crop rotation effect was analyzed by comparing SQ indicators between rice/rape rotation soil and cotton/barley rotation soil. An overall SQI was calculated to examine whether plant biomass indices exactly responded to the SQI value. Results indicated that cultivation had significant effect on some soil profile characteristics, including SOM, SOCD, AP, CEC, AK, ECe, and I (f). Crop rotation systems also had significant influence on some SQ indicators. Compared with cotton/barley rotation soil, rice/rape rotation soil was characterized by higher organic matter, undifferentiated nutrient storage and salinity/alkalinity, lower water accommodation and infiltration, and adverse groundwater conditions. Cotton/barley rotation had higher SQI values over rice/rape rotation (0.523 vs. 0.422). SQ indicators of SAR(e), ECe, and WTg contributed the most to the overall SQI value for each rotation system. Plant biomass indices significantly correlated with the SQI values for both rotation systems, suggesting that the SQI values essentially reflected the status of SQ. Such results allowed us to conclude that cotton/barley rotation system contributed more to the improvement of SQ than rice/rape rotation system in coastal farming area. Also, we suggested SOCD, AK, rho (b), WTg, and ECg as the minimum data set for SQ assessment, as they had potential in discriminating the effect of rotation systems on SQ between the rotation systems used here.