We analyzed factors regulating soil organic carbon (SOC) storage across different ecosystem types in NWT, Canada; white spruce forest (WSF) on upland soil, black spruce forest (BSF) and tundra (TND) in lower position. Field incubation of cellulose filter paper and root litter showed that water flooding and cold climate retarded decomposition of organic matter in BSF and TND. The warmer and aeration condition in sandy upland soil of WSF enhanced organic matter decomposition. The SOC storage in BSF and TND soils were significantly greater than in WSF soil. The low temperature and water saturation in lowland can increase SOC storage in permafrost soils.