As the regulator of water and nutrient changes in the active layer after permafrost degradation, root signaling substances affect the plant–soil carbon allocation mechanism under climate warming, which is a key issue in the carbon source/sink balance in permafrost regions. To explore how plant root signaling substances regulate carbon allocation in plants and soils under permafrost degradation, the changes in carbon allocation and root signaling substances in the plants and soils of peatland in different permafrost regions at the time of labeling were studied by in situ 13C labeling experiments. The results showed that the fixed 13C of Larix gemlini, Carex schumidtii, and Sphagnum leaves after photosynthesis was affected by permafrost degradation. In regions with more continuous permafrost, the trend of the L. gemlini distribution to underground 13C is more stable. Environmental stress had little effect on the 13C accumulation of Vaccinium uliginosum. Nonstructural carbohydrates, osmotic regulatory substances, hormones, and anaerobic metabolites were the main root signaling substances that regulate plant growth in the peatlands of the three permafrost regions. The allocation of carbon to the soil is more susceptible to the indirect and direct effects of climate and environmental changes, and tree roots are more susceptible to environmental changes than other plants in isolated patches of permafrost regions. The physical properties of the soil are affected by climate change, and the allocation of carbon is regulated by hormones and osmotic regulators while resisting anoxia in the sporadic regions of permafrost. Carbon allocation in discontinuous permafrost areas is mainly regulated by root substances, which are easily affected by the physical and chemical properties of the soil. In general, the community composition of peatlands in permafrost areas is highly susceptible to environmental changes in the soil, and the allocation of carbon from the plant to the soil is affected by the degradation of the permafrost.