In China, deep tillage (DT; to >20 cm soil depth) has increased crop yields by improving soil properties, while no-tillage (NT) has been recommended to reduce the labor and machinery costs. Local farmers are willing to adopted rotary tillage (RT; harrowing to 10–15 cm depth) for easy management. However, the effects of these tillage management methods on agronomic productivity, greenhouse gas (GHG) emissions, soil organic carbon (SOC) sequestration, and economic return have not been quantified systematically, and their effectiveness remains in question. Here, we present a meta-analysis of the effects of these methods using 665 paired measurements from 144 peer-reviewed studies. The results indicated that DT significantly increased crop yields by 7.5% relative to RT, and even greater increases were observed in regions with low temperatures and with a wheat cropping system. In contrast, NT resulted in a yield reduction of 3.7% relative to RT, however, controlling for the appropriate temperature and long extension duration (>15 yr) could reduce yield losses and even increase the yield. Both DT and NT significantly enhanced SOC sequestration relative to RT. Adoption of DT would lead to both higher total GHG emissions (N2O and CH4) and increased energy costs, while NT reduced GHG emissions. DT management exhibited a positive net profit for all cropping systems; NT decreased the net profit for rice and wheat but increased the profit for maize. Our study highlighted the agronomic, environmental, and economic benefits and trade-offs for the different tillage methods and should enable investors and policymakers to ensure the best tillage management decisions are made depending on the location-specific conditions.