Subsurface application of organic ameliorant is a novel strategy for stimulating salt leaching out of profile and increasing saline soil fertility and microbial activities. However, it is unclear how microorganisms regulate the contribution of microbial-derived C to SOC sequestration under subsurface organic ameliorant in saline soils. Thus, a 3-year field experiment was done and included three treatments (control, surface organic ameliorant (humic acid (4.5 t ha−1) and manure (30 t ha−1)) at 0–15 cm (SF), and subsurface organic ameliorant application at 15–30 cm (SSF)) organized into a randomized complete block design. SSF increased soil organic carbon (SOC) stocks at 0–30 cm, while SF only affected SOC at 0–15 cm. SOC stock at 0–45 cm under SF increased by 13% and under SSF by 22% relative to the control. The accumulation of SOC was explained by high fungal necromass C under organic amendments. Random forest and structural equation modeling revealed that increased fungal and bacterial necromass C at 0–30 cm soil under SSF and SF is caused by high microbial C use efficiency, the dominance of r-strategist bacteria, and increased fungal richness. The increase of microbial necromass C at 0–30 cm under SSF was higher than under SF (27–45 vs 25–37% compared to Control), which was explained by the raised bacterial necromass and its incorporation into mineral-associated organic matter (MAOM). High amounts of root exudates in deep soil under SSF also promoted fungi turnover and accelerated fungal necromass formation at 30–45 cm. Overall, subsurface amelioration of saline soils enhanced C sequestration by stabilizing microbial necromass in MAOM. © 2025 Elsevier B.V., All rights reserved.