Achieving carbon peaking and carbon neutrality requires coordinated action across macro, meso, and micro levels. For Chinese firms, reducing carbon emissions and controlling carbon costs are important challenges. Using Nanjing Iron and Steel Co., Ltd. (NJ Steel) as a case, this study proposes a two-dimensional “carbon flow–value flow” cost control method that traces carbon-containing material and energy inputs, transformation, and emissions through steel production, maps these flows to internal resource transfer costs and external environmental damage costs, and identifies process-level control points and optimization measures. Carbon flow analysis indicated that coking, ironmaking, and steelmaking are high-emission processes. Value flow analysis showed that these processes also incur high carbon costs and are therefore key control points. Within the process-level quantitative boundary and simulated optimization scenarios, internal resource transfer costs and external environmental damage costs were RMB 1,176 million and RMB 1,442 million lower than baseline, respectively. After accounting for technical retrofit investment and key parameter uncertainty, carbon cost reductions ranged from approximately RMB 1,879 million to RMB 3,941 million across the sensitivity scenarios. The findings provide practical guidance for enterprises seeking to strengthen carbon emissions management, optimize carbon cost control, and advance their low-carbon transition.