Improvements of soil organic carbon and reduction of carbon footprint are critical for the sustainability of agricultural production system. In a 14-year (2006–2020) field experiment, we assessed the effects of conservational (reduced/zero) tillage and residue management (incorporation/retention) (CsT+RM) practices on carbon input, carbon sequestration, productivity and profitability rice-wheat system (RWS) in western Indo-Gangetic Plains (IGP) of India. Experiment consisted one scenario of conventional tillage (Sc-1: Puddle transplanted rice - conventional tilled wheat); and four scenarios of CsT+RM that are, Sc-2: Reduce tilled direct seeded rice (RTDSR) - reduce tilled wheat (RTW); Sc-3: RTDSR-RTW + 1/3rd residue incorporation (RI); Sc-4: Zero tilled direct seeded rice (ZTDST)-zero tilled wheat (ZTW); and Sc-5: ZTDSR-ZTW + 1/3rd residue retention (RR). Overall, 14-years mean DSR yield significantly (p < 0.05) lowered (9.0–22.0 %), and wheat yield significantly increased (4.4–9.2 %) in CsT+RM practices as compared to Sc-1. The mean RWS yield lowered by 1.0–3.8 % in reduced tillage and 6.3–9.3 % in zero tillage, along with 10.9–17.4 % lower cost of cultivation and nonsignificant higher return over variable cost under CsT+RM practices. The sustainable yield index of DSR was lower (0.50–0.58), and wheat was higher (SYI; 0.65–0.69) in indicating the low sustainability of DSR and better sustainability of wheat in CsT+RM. The long-term CsT+RM caused net enrichment in SOC stock by 2.4–21.0 %, and carbon sequestration from 9.9 % to 87.0 % in different scenarios over Sc-1. In order to counterbalance the loss of SOC and maintain its level, a critical amount of 1.17 Mg C ha−1 yr−1 need to be added into the soil. The CsT+RM thus enhanced the SOC stock and sequestration in the soil and provided at par system yield in reduced tillage and lower yield in zero tillage grown RWS. Further, better management of DSR including development of suitable genotype for direct seeding, ensuring uniform crop establishment, weed and micronutrient management under reduced/zero tillage is needed for long-term sustainability of DSR-ZTW system in the western IGP of India.