Soil health indicators linked to environment services such as nutrient management, crop practices, and biodiversity. 14 soil health indicators were measured and compared in our study to clarify the impact of different cropping systems on soil quality. The main comparisons were conducted between perennials, annuals, and cover cropping, while the tillage system and fertilization were also applied in the analysis. The regression and path analysis revealed that improved soil carbon was consistently associated with greater moisture, wet aggregate stability, and carbon mineralization. The main factor for clustering treatments based on indicators was N fertilization and tilling operation according to Euclidean distance that was applied to measure the similarity of the groups. Although perennials and cover crops recorded sequestering more carbon and improving TC, corn and corn-sorghum in rotation crops showed a worse impact on soil PH and bulk density (BD). Non-tillage practices significantly increased wet aggregate and soil moisture. The combination of TC field measurements with long-term cropping systems information has improved our understanding of how different cropping practices influence soil health improvement in full profile. It can develop appropriate and cost-effective agricultural management activities, maintains or improves carbon soil accumulation to guide farmer decision-making and ultimately advance food and nutritional security.