While it is recognized that the accumulation and turnover of soil organic carbon (SOC) is driven by plant inputs and their subsequent microbial-mediated transformations, the roles of plant residue chemistry and microbial processes in controlling SOC dynamics under different fertilizer application regimes have not been well explored. In the present study, amino sugars and lignin phenols were used as biomarkers to investigate the changes in microbial necromass and plant-derived components in a 30-year cultivated Mollisol (0–20 cm) in response to different fertilizer application treatments, including synthetic fertilizers (NPK, 165 kg N ha−1, 82.5 kg P2O5 ha−1, and 82.5 kg K2O ha−1 per year), pig manure at two application rates of 30 and 60 t ha−1 per year, and combinations of manure and synthetic fertilizers (30 or 60 t ha−1 manure per year plus 165 kg N ha−1, 82.5 kg P2O5 ha−1, and 82.5 kg K2O ha−1 per year). Compared with the unfertilized plot (Control), 30-year application of synthetic fertilizers increased microbial biomass (161%) and amino sugar production (19.7%), but did not alter lignin phenol and SOC concentrations despite the increased plant input. Comparatively, long term manure applications increased the concentration of SOC (30.8–70.9%), as well as that of amino sugars (82.9–107%) and lignin (96.8–212%) in soil. Nevertheless, despite the enhanced microbial biomass from low to high manure application rate, the proportion of amino sugars in the SOC decreased, reflecting a diluted contribution of microbial necromass in SOC pool buildup at high-rate manure application. On the contrary, the proportions of lignin phenols in the SOC in the manure treatments, as well as the ratios of lignin phenols and amino sugars (0.26–0.42), were larger than that in the NPK treatment (0.22) and increased with increasing manure application rate. Therefore, the manipulation of synthetic or organic fertilizer on SOC dynamics is associated with differential accumulation of microbial necromass and plant lignin in agro-ecosystems. The manure amendment enhanced the contribution of plant-derived components more than microbial necromass to long term SOC accumulation.