China’s crop production sector holds significant potential for emission reduction and carbon sequestration， playing a crucial role in achieving the “Dual Carbon” goals. Based on county-level data across China， this study employs a fixed effects model to analyze the impact of FOS on intensity of carbon emission， carbon sequestration， and net carbon sequestration in crop production. A simultaneous equations model is further applied to examine influencing pathways through multidimensional factors， including input intensity， cropping structure， and crop yield. The results are as follows： 1） As FOS expands， the net carbon sequestration intensity of crop production follows a “U-shaped” curve， with the turning point occurring when per capita farm operation scale reaches 2.25 hectares. Specifically， carbon emission intensity exhibits an “inverted U-shaped” trend， while carbon sequestration intensity shows a “U-shaped” pattern， with the latter dominating the net carbon sequestration dynamics. 2） The “inverted U-shaped” trajectory of carbon emission intensity is primarily driven by fertilizer input intensity， which similarly follows an “inverted U-shaped” response to FOS expansion. 3） The transition in cropping structure from “non-grain-oriented” to “grain-oriented” practices， induced by FOS expansion， is the key factor behind the “U-shaped” trend in carbon sequestration intensity. Given that the carbon sequestration effect of crop production far outweighs its emission effect， this structural shift also becomes the decisive factor for the “U-shaped” net carbon sequestration intensity. Therefore， accelerating the transition to large-scale agricultural operations is essential for long-term low-carbon development in crop production. However， during the initial stages of this transition， targeted policy interventions are necessary to mitigate potential adverse impacts on emission reduction and carbon sequestration.