Microorganisms play a crucial role in the accumulation of soil organic matter through microbial residue deposition. This study investigates how microbial life strategies—high growth yield (Y), resource acquisition (A), and stress tolerance (S)—affect microbial necromass carbon (MNC) and soil organic carbon (SOC) accumulation in rice-cultivated saline soils over a millennium. We observed a significant increase in SOC with cultivation duration: from 1.8–5.9 g·kg−1 after 50 years to 4.4–9.5 g·kg−1 after 1000 years. Soil pH and electrical conductivity (EC), as indicators of salinity, decreased during cultivation, while available N, P nutrients and the SOC followed an opposite trend. Initially, high salinity levels and low nutrient content hindered microbial growth and activity, thereby limiting MNC accumulation. In the early stages of soil cultivation (50 years) under salt stress (EC > 950 μm·cm−1), the S-strategists (e.g., Lysobacter, Hydrogenophaga) were favored, resulting in the lowest accumulation of microbial necromass. Between 200 and 500 years of cultivation, A-strategists (e.g., Polaromonas, Cavicella) became dominant, increasing production of extracellular hydrolytic enzymes for nutrient acquisition. After 1000 years, reduced salt stress and increased nutrient availability led to a shift to Y-strategists (e.g., Rhodanobacter, Nectriaceae), characterized by the highest level of microbial necromass and its contribution to the SOC pool. In conclusion, soil microorganisms shifted from S- to A-strategists and later to Y-strategists with decreasing salinity and increasing nutrient contents, resulting in greater MNC accumulation and SOC sequestration after a millennium of rice cultivation. © 2025 Elsevier B.V., All rights reserved.