The majority of related research has traditionally focused on examining the individual influences of national governance capacity and technological innovation on carbon emissions and economic performance, neglecting the effects and influence mechanisms on carbon efficiency within agricultural supply chains, which is not conducive to advancing a low-carbon transition that includes agricultural concerns. This study addresses these gaps by investigating the correlation between national governance capacity (considering voice and accountability, political stability and absence of violence/terrorism, government effectiveness, regulatory quality, rule of law and corruption control) and agricultural supply chain carbon efficiency and investigating the influence mechanism and mediating role of technological innovation. The relevant findings are twofold. 1) The impact of national governance capacity and its components on agricultural carbon efficiency follows an inverted U-shaped curve. 2) Technological innovation can act as a mediator between national governance capacity and select factors of voice and accountability, government effectiveness and regulatory quality to enhance agricultural supply chain carbon efficiency. The findings offer valuable insights for policymakers and managers in agricultural supply chain enterprises seeking to transition towards low-carbon agriculture.