<p>Agricultural mechanization has benefitted food security in China, but carbon dioxide (CO₂) and air pollutant emissions from fuel combustion are often overlooked. Here we show that emissions of CO₂ and air pollutants from agricultural machinery increased nearly sevenfold and four- to sevenfold, respectively, during 1985–2020, driven largely by rapid advancement in the mechanization level. If unabated, annual emissions of CO₂, PM_2.5 and NO_<i>x</i> from agricultural machinery in 2050 could reach 213.6 Mt, 55.4 Gg and 902.8 Gg, contributing ~21%, ~4% and ~17% of China’s total emissions under a dual-carbon goal scenario, respectively. However, adoption of renewable energy sources could mitigate 65–70% of these emissions. Our study highlights that China’s agricultural machinery could become a large source of emissions that—without mitigation—may hinder China’s carbon neutrality targets and degrade air quality.</p>