Reducing greenhouse gas (GHG) emissions in crop production while ensuring emission equity is crucial for sustainable agriculture in China, yet long-term large-scale data on GHG emissions intensity (GEI) are limited. Using an extensive dataset based on surveyed farm households (n > 430,000 households) from 1993 to 2020, we reveal that 2015 was a turning point for GEI levels, which dropped 16% in 2020, while inequality—measured as average GHG emissions per unit planted area—increased 13%. The key driving forces behind such trends included farmland input, all other inputs, agricultural labour input and total factor productivity but not capital input. Notably, farmland input and all other inputs contributed to 80% of the inequality, while contribution of total factor productivity gradually declined and was replaced by migration-induced agricultural labour input differences. Reducing GEI levels and guarding against widening inequality require optimizing production factor inputs.