Integrated crop-livestock system (ICLS) is an alternative that can help in intensifying food production while benefiting the environment. However, the assessments of the impacts of ICLS on the soil and economic benefits relative to specific environments in South Dakota are still lacking. This study was to assess the effects of ICLS on soil health and economic benefits under a corn (Zea mays L.)-soybean (Glycine max L.)-rye (Secale cereale L.) rotation in South Dakota. Cover crops blends were planted after the rye crop, and grazing treatments (with and without) were applied after the cover crops establishment in 2015-2016. Data from this study indicate that most soil properties are not negatively impacted by grazing. However, the grazing increased soil bulk density (BD) and decreased soil organic carbon (SOC) and soil water retention (SWR) compared with the ungrazing. The effect of grazing on corn yield was not significant. The cover crops did not impact the pH, electrical conductivity (EC), total nitrogen (TN), β-glucosidase, acid hydrolysis carbon fraction, microbial biomass carbon, and SWR, but impacted the SOC, hot/cold water carbon fraction, BD, infiltration rate (qs) in some phases and depths. The effects of different cover crop blends on corn yield were not as strong. The economic analysis showed that implementing ICLS increased the profit of the farm by $17.23 ac−1 in the first year and $43.61 ac−1 in the second year. These findings indicate that ICLS practices with proper management benefit soil health and producer income.