Irrigated agriculture has tripled since 1950, accounting for 20% of the global arable land and 40% of food production. Irrigated agriculture increases food security yet has controversial implications for global climate change. Most previous studies have calculated carbon emissions and their composition in irrigated areas using the engineering approach to life-cycle assessment. By combining life cycle assessment (LCA)-based carbon emissions accounting with econometric models such as multiple linear regression and structural equation modeling (SEM), we conducted an interdisciplinary study to identify the influencing factors and internal mechanisms of the carbon footprint (CFP) of smallholder crop cultivation on irrigation reform pilot areas. To this end, we investigated corn and potato production data in the 2019–2020 crop years for 852 plots of 345 rural households in six villages (two irrigation agriculture pilot villages and four surrounding villages as controls) in Southwest China. The crop CFP in the irrigation agriculture pilot areas was significantly lower than in non-reform areas. Irrigation reforms mainly impacted the crop CFP through four intermediary effects: the project (implementation of field irrigation channels), technology (improving adoption of new irrigation technologies), management (proper irrigation operation and maintenance), and yield effects. All effects inhibited the CFP, except for the project effect that promotes carbon emissions. Among them, yield increase has the greatest impact on reducing CFP, followed by management and technology effects. Furthermore, planting practices, individual characteristics, and plot quality significantly impacted the crop CFP. This study has policy implications for understanding the food security–climate nexus in the food production industry.