Under the global climate governance framework, the Paris Agreement and the China–U.S. Glasgow Joint Declaration established a non-negotiable target of limiting 21st-century temperature rise to 1.5 °C. To date, over 130 nations have pledged carbon neutrality by mid-century, with agricultural activities contributing 25% of global greenhouse gas (GHG) emissions. The spatiotemporal dynamics of these emissions critically determine the operational efficacy of carbon peaking and neutrality strategies. While China’s Nationally Determined Contributions (NDCs) commit to achieving carbon peaking by 2030, a policy gap persists regarding differentiated implementation pathways at the county level. Addressing this challenge, this study selects the Three Gorges Reservoir (TGRA)—a region characterized by monocultural cropping systems and intensive fertilizer dependency—as a representative case. Guided by IPCC emission accounting protocols, we systematically evaluate spatiotemporal distribution patterns of agricultural CH₄ and N₂O emissions across 18 county-level units from 2006 to 2020. The investigation advances through two sequential phases: Mechanistic drivers analysis: employing the STIRPAT model, we quantify bidirectional effects (positive/negative) of critical determinants—including agricultural mechanization intensity and grain productivity—on CH₄/N₂O emission fluxes. Pathway scenario prediction: We construct three developmental scenarios (low-carbon transition, business-as-usual, and high-resource dependency) integrated with regional planning parameters. This framework enables the identification of optimal peaking chronologies for each county and proposes gradient peaking strategies through spatial zoning, thereby resolving fragmented carbon governance in agrarian counties. Methodologically, we establish a multi-scenario simulation architecture incorporating socioeconomic growth thresholds and agroecological constraints. The derived decision-support system provides empirically grounded solutions for aligning subnational climate actions with global mitigation targets.