Plant residue is ultimately the source of soil organic matter but occurs as a continuum from relatively fresh plant tissue to highly evolved components. Nevertheless, the extent to which crop residue accumulates as plant tissue versus microbial necromass in conservation agricultural systems is still uncertain. A 12-year conservation tillage experiment with maize additions of zero, half and full harvest was conducted in Northeast China. Soil samples in the 0–10 cm depth were collected at 1–4 year intervals. The microbial residue biomarker amino sugar and plant component biomarker lignin phenol were quantified to trace the dynamics of microbial necromass and plant debris. Compared with the initial value, the content of amino sugar increased exponentially to 21–45% and approached steady-state equilibrium after 12 years of maize straw mulching, indicating the existence of “microbial carrying capacity” under repeated plant residue addition. With prolonged duration of conservation tillage and increasing rate of maize straw return, the ratio of amino sugar to lignin phenol decreased from 6.2 to 1.7, accompanied by a decreased degree of lignin side-chain oxidation, indicating that organic input enhanced the selective retention of fresh plant lignin to a larger extent than microbial necromass. The build-up of the SOC pool under conservation tillage was critically controlled by the functional complementation of microbial- and plant-derived components. Maize straw input was able to enhance the contribution of microbial necromass to SOC stabilization by increasing fungal necromass accumulation, while the retention of lignin-like plant debris enlarged the SOC pool capacity and potentially maintained the decomposability of SOC in the long term.