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Soil microbes’ activity is very important for forming of the nutrient stock and, soil structure, as well as the carbon cycle simulation. This is particularly crucial for deep soil layers. Effect of soil microbes on the rate of accumulation and decomposition of the soil organic carbon (SOC) has been found for different regions. However, it is known still a little on the SOC performance for different decomposition rates and its relation to the microbial activity in the saline-alkali desert ecosystem. Therefore, the main task of our research was investigation of interrelation between the soil organic carbon and microbial carbon (SMC) at different depths in the original saline-alkali Gurbantunggiit Desert. Our results showed in the soil vertical profile, (i) SMC and SOC presented a very significant positive linear correlation (R-2 = 0.63, P = 0.0003); (ii) SMC exhibited two obvious changed-interfaces - 20 cm and 80 cm, the SMC at depth of 0-20 cm, 20-80 cm and 80-500 cm was 2.24-3.06, 0.19-0.72, and 0.0017-0.0097 mg kg(-1), respectively; (iii) in the depth of 0-20 cm and 20-80 cm, the SMC had highly significant difference (P < 0.0001) and at 20-80 cm and 80-500 cm, significant difference (P = 0.013); (iv) according to the soil division based on the SMC, SOC also had some certain stratification; (v) organic carbon layers can be respectively defined according to different microbial activities as active, inert, and stable organic carbon pool. Therefore, these three kinds of organic carbon pools can be quantitatively measured by analyzing their location at different depths of the soil profile.