Modern agriculture, driven by diesel-fed machinery, is both energy and carbon-intensive, primarily due to the improper use of inputs. Designing a production module with lower carbon emissions, greater productivity, and enhanced energy use efficiency is crucial for achieving the environmental sustainability. Conservation agriculture based integrated crop management (ICMs) practices have shown promise in improving the productivity, energy-use, and reducing the carbon emissions. In our extensive long-term field study, we explored the crop yields, energy use, and carbon linkages of a maize-wheat rotation under different ICMs practices. Eight ICMs were evaluated over the course of nine consecutive years, which included ICM1&2: conventional (CT) flat-bed maize and wheat, ICM3&4: CT raised bed maize fb wheat without residues, ICM5&6: conservation agriculture (CA)-based double zero tilled (ZT) maize fb ZT wheat with residues and ICM7&8: CA-based triple ZT maize and wheat with residues and green manures. Our results indicated that the system productivity under CA-based ICMs was 16.5–22.9% greater than that under the CT-based ICM1-4. CA based ICM5-8 (125.2–131.5 × 103 MJ ha−1) needed higher energy input than CT-based ICM1-4 (32.7–39 × 103 MJ ha−1), with 76–80% shared by renewable crop residues. Furthermore, the CA-based ICMs recorded significantly higher levels of specific energy, human energy profitability, non-renewable energy use efficiency, and nutrient energy use efficiencies compared to CT-based. Likewise, the CA-based ICMs produced 12.5% more total output energy than the CT-based ICMs. In contrast, the CT based ICMs demonstrated, energy productivity, higher net energy returns and energy profitability. Compared to conventional ICMs, CA-based ICMs produced a 23–36% reduction in spatial carbon emissions and a 31–44 % reduction in yield-scale emissions. Nevertheless, the CA-based practices recorded the higher C- output, C- sustainability and C- efficiency ratio. Greenhouse gas intensity (GHGI) was 33.3–76.2% greater with the ICM1-4 practices than with the ICM5-8 practises. Thus, the present study proposed that adopting the integrated crop management practices based on the conservation agriculture could prove to be productive, as well as carbon and energy-use efficient approach for the maize-wheat rotation. This approach is envisioned to make substantial contributions to both food security and environmental sustainability.