Both warming and nitrogen (N) addition affect the chemistry and characteristics of soil organic matter (SOM). However, their interactive impacts on molecular compositions and origins (plant- or microbial-derived) in agroecosystems are indeterminate. A nine-year field trial study in Northern China was undertaken to quantify the effects of warming (+2 °C), N addition (315 kg N ha⁻¹ yr⁻¹), and their interaction on SOM content and its composition, using biomarkers (i.e., free lipids, lignin phenols and amino sugars) and ¹³C NMR. Despite insignificant changes in bulk SOM content, the characteristics (i.e., molecular constituents, lability and source origin) were significantly influenced by warming and/or N addition in surface soil (0–10 cm), but not in the subsurface soil (10–20 cm). The SOM was composed of approximately 18–27% microbial residues with the bulk derived from fungi (up to 4–fold higher than bacteria). Warming alone reduced total free lipids (mainly short-chain lipids, <C₂₀) by 21%, but increased lignin phenols (vanillyls and syringyls) by 37% and microbial residues (quantified as amino sugars) by 31%. Nitrogen addition alone increased lignin phenols by 28% and microbial residues by 30% in surface soils but had a limited effect on free lipids content. Combined warming and N addition additively increased total free lipids by 40% and lignin phenols by 42% and the ratio of fungal/bacterial microbial residues in the surface soils. Collectively, our study results suggest that warming and nitrogen addition have a synergistic positive effect on SOM persistence in temperate agroecosystem via accrual of lignin phenols and microbial residues.