The variability of soil carbon and nitrogen and the lack of information regarding the properties of deep soils in alpine permafrost regions hinder our understanding of ecosystem responses to climate change. The objective of this study was to examine the effects of pedogenesis and soil physicochemical parameters on the distributions of soil carbon and nitrogen and their characteristics of alpine meadows in permafrost regions. The results showed that pedogenesis was an important factor in the distribution of soil organic carbon (SOC) and total nitrogen (TN) in both the active layers and deep soils. The average water-soluble organic carbon (WSOC) content in the permafrost layer was higher than that of the active layer, which implied that the carbon pool in the permafrost layer was easily decomposable. Soil pH was an important factor that influenced soil inorganic carbon (SIC), which was closely associated with SOC in deep soils. The significant negative relationships between the SIC, pH and C/N ratios in permafrost regions implied that SIC can play an important role in the turnover of SOM and TN. •We study the effects of pedogenesis and soil physicochemical parameter on carbon.•Labile carbon content in permafrost layer was higher than that in active layer.•SIC has an effect on distribution of organic carbon and nitrogen in deep layers.