Hummock-hollow microtopography is common in the northern peatlands of the world, but its effects on soil organic carbon (SOC) components are still poorly understood. In this study, we investigated effects of microtopography on SOC stocks and soil labile organic carbon (LOC) fractions in a sedge peatland in Changbai Mountain in northeast China. We found that SOC and soil LOC fractions had much heterogeneity in microtopography. SOC concentration in hummocks was significantly higher than under hummocks and in hollows. On average, the total SOC stock to a depth of 0.3 m below the ground surface was 19.00 kg C/m². Fifty six percent of the total SOC stock was stored in soils in and under hummocks, despite the hummock only covering 30% of the total area. Light fraction organic carbon (LFOC), easily oxidizable organic carbon (EOC), microbial biomass carbon (MBC) and dissolved organic carbon (DOC) in hummocks were significantly higher than under hummocks and in hollows. Redundancy analysis (RDA) identified that SOC explained most variations in soil LOC fractions (59.6%), followed by soil total phosphorus (7.4%) and soil water content (6.6%). Our findings indicate that the hummock is an important carbon pool in the sedge peatland. Hummock-hollow microtopography creates heterogeneity in hydrological conditions and soil physicochemical properties, and thus influences SOC stocks and soil LOC fractions at a small scale. This study highlights the importance of microtopography in carbon storage and cycling and has direct implications for the assessment of the carbon sequestration function in northern peatlands.