In the interior of Xizang (Tibetan) plateau, the active tectonics are primary marked by north trending rifts in southern Tibet. Gulu—Yadong rift is the largest and longest extensional rift in South Tibet. The rift valley has a number of hot spring clusters distributed from south to north, and hot springs such as Kangbu, Kangma, Zhadang, and Mengze are concentrated in the southern Rift Valley. Based on the geochemical characteristics of rare earth elements in hot springs in the southern Gulu—Yadong rift valley, this paper discusses the main controlling factors of rare earth elements. The results show that the southern hot springs are weakly acidic—alkaline hot springs. The total rare earth elements (ΣREE) in hot spring of Gulu—Yadong rift ranged from 1.41 to 46.18 ng/L, which is at a low level compared with alkaline hot springs in the world. Most samples show LREE (light rare earth element) and HREE (heavy rare earth element) relative depletion, MREE (medium rare earth element) enrichment and negative Ce anomaly. Adsorption and desorption processes of Fe/Mn minerals to REEs can increase or decrease REE concentration. REECO3+and REE(CO3)2- is the major speciation, and affect the differentiation of rare earth element. The REE distribution pattern of most hot springs in Yadong area is affected by iron rich sediments, resulting in the preferential release of MREE into aqueous solution. The distribution characteristics of rare earth elements in Kangma hot spring are affected by water—rock reactions, including the dissolution of iron- rich sediments and the dissolution of local basic magmatic rocks. Negative Ce anomalies may result from oxidative scavenging process of Ce. pH, Fe/Mn minerals, carbonate complexes and water—rock reaction all affect the REE distribution of hot springs.