The freezing and thawing process is a unique feature of the alpine permafrost ecosystem, which controls the growth of microorganisms and alpine meadows, and plays a vital role in animal husbandry development, ecosystem functions and services. Meanwhile, the freezing and thawing process is also affected by external environmental factors, and its spatial differences are very significant, especially in the regions over 5000 m a.s.l. In this study, the freezing and thawing process periods of the Cuoma Township (CM), Xiangmao Township (XM) and Xiaotanggula Mountain (XTGL) sites in the Nagqu River Basin are divided, the effects of altitude, vegetation coverage, air temperature, and organic matter content on the freezing and thawing process are analyzed, the main influencing factors are discussed. The results show that in the regions over 5000 m a.s.l, the thaw initiation period (TIP) starts in early April, the entirely thawed period (ETP) starts in end of May, the freeze initiation period (FIP) starts in end of October, and the entirely frozen period (EFP) starts in early November. Compared with the regions below 5000 m a.s.l, FIP and EFP in the regions over 5000 m a.s.l start earlier, the TIP starts later and the freezing rate is faster. Organic matter content is the main influencing factor during FIP and EFP, and air temperature is the main influencing factor during TIP and ETP. This study is helpful to clarify the changes of freezing and thawing process in the regions over 5000 m a.s.l, and also provides theoretical support for ecological protection and restoration.