The Source Areas of the Yangtze and Yellow Rivers (SAYYR), which is located in the transitional zone from predominantly continuous permafrost to seasonally frozen ground, is one of the most important cold regional ecological barriers in China. The negative temperature and frozen environment facilitate the long-term existence of frozen ground, accordingly inhibiting soil microbial activities and the mineralization process of soil organic matter, resulting in high carbon and nitrogen contents in the near-surface shallow soils. However, it is still unclear how the soil carbon and nitrogen content respond to the spatial distribution pattern of the variability in the thermal state of permafrost and environmental factors. In this study, eleven plots were investigated at four different typical kinds of frozen ground (seasonally frozen ground, island permafrost, discontinuous permafrost, and predominantly continuous permafrost) in the SAYYR. We conducted plant quadrat survey and soil sampling from different depths. After analyzing the soil carbon and nitrogen content, we explore the distribution of soil organic carbon (SOC), total nitrogen (TN), C/N, and key factors that influence the distribution of soil organic carbon (SOC), total nitrogen (TN), and C/N. The environmental factors include mean annual ground temperature (MAGT), active layer thickness (ALT), altitude (ASL), soil depth (SD), vegetation characteristics, and soil pH. The results show that: (1) the contents of SOC, TN, and C/N were positively correlated with altitude but negatively correlated with MAGT, being characteristics of an obviously vertical pattern, with the highest values coming from the predominantly continuous permafrost region, and the lowest values coming from the seasonally frozen ground region; (2) With the increase of soil depth, the overall decreasing rates of SOC, TN, and C/N were 58.45%, 36.96%, and 17.01%, respectively; (3) The SOC and TN contents were positively correlated with fractional vegetation (FVC) (P≤0.05), but significantly negatively correlated with soil pH (P≤0.01); and; (4) The redundant analysis showed that soil pH, MAGT, ALT, SD, and FVC in permafrost were the dominant environmental factors for the spatial distribution and depth patterns of SOC, TN, and C/N. Our study provides data support for clarifying the spatial distribution characteristics between SOC, TN, and C/N, and the determinations of the thermal stability of permafrost on soil carbon and nitrogen emission under climate warming in the SAYYR in the future. Thus, our study will also shed light on the prediction of soil carbon and nitrogen change in permafrost region, which is one of the biggest carbon pools of great uncertainty.