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.