Background and aims <p>Soil organic matter (SOM) is crucial for the productivity of greenhouse soils, yet its chemical composition over time has not been well explored, particularly under high-intensity tillage practices. This study analyzed the dynamic changes in the chemical composition of SOM based on 78 soil samples collected across different cropping years in Eastern China.</p> Methods <p>The study site features a typical temperate continental monsoon climate, and the surveyed greenhouse and farmland soils are all cinnamon soils. Soils were categorized into four groups based on land use and cropping years. Fourier transform infrared (FTIR) spectroscopy was used to assess the chemical composition of SOM.</p> Results <p>High-intensity greenhouse cultivation induces significant and non-linear alterations in SOM chemical composition. The specific manifestations are the selective consumption of labile functional groups and the gradual intensification of SOM aromatization. Compared to field soils, polysaccharide-C decreased by 5.47% and aromatic-C/aliphatic-C increased by 29.0% in greenhouse soil cultivated for more than 15&#xa0;years. The continuous high-intensity cultivation with facilities intensifies the enrichment of soil nutrients, which drives the intensified aromatization of the soil.</p> Conclusion <p>The shift from field to greenhouse cultivation increased SOM stability, with the depletion of unstable functional groups being the major driver of this change. Although greenhouse cultivation have receive long-term application of organic fertilizer to replenish SOM rich in easily decomposable functional groups, this did not alleviate the aromatization of greenhouse soils. These results enhanced our understanding of how agricultural cultivation and management practices affect the SOM stability over time.</p>