In order to explore thegenesis of hydrocarbon geochemical anomalies and gas source conditions of hydrocarbon source rocks in the permafrost region of southern Qinghai, we analyze the content of acidolysis hydrocarbon, fluorescence spectrum, and methane carbon isotope of core samples from the TK- 1 borehole in the Kaixinling permafrost region. We also examine the vertical migration characteristics of these samples and discuss the causes of hydrocarbon geochemical anomalies. Our research delves into the relationship between hydrocarbon anomalies and the fractures or fracture zones, hydrate stability zones, and the process of hydrocarbon formation. By analyzing this relationship, we aim to understand the significance of geochemical anomalies in hydrocarbon migration and accumulation. The results show significant geochemical anomaly enrichment of hydrocarbons at depths of 62~80 m, 112~119 m, 150~169 m, and 254~350 m. Based on the hydrocarbon composition, parameter ratio (C1/ΣC1- 5, C1/ΣC2- 5, C1/ΣC2- 3, iC4/nC4, etc.), and methane carbon isotope (δ13CPDB) characteristics, we conclude that the hydrocarbons are mainly pyrolytic in nature. This includes oil- type cracking gas, condensate- associated gas, coal- derived gas, and a small amount of inorganic gas. Furthermore, the coal series source rocks of the Permian Nayixiong Formation have reached the high- to- over- mature stage. The hydrocarbon generation and expulsion of gas during thermal evolution might be an important source of gas for hydrate formation. The “baffle effect” of the permafrost zone forms a strong geochemical anomaly of hydrocarbons beneath the permafrost layer, which can be used as an indicator of natural gas hydrates and abnormal phenomena. Additionally, the content of acidolysis hydrocarbon components in the fractures or fracture zones is relatively high. With the change of depth, hydrocarbon components show an obvious “color layer effect” indicating that the fractures or fracture zones exert a certain control effect over the migration and accumulation of hydrocarbons.