Abstract: Helium is a rare resource and is widely used in the high-tech field. However, the helium supply in China heavily depends on imports. The Huazhou exploration area of Gushi Sag in Weihe basin is a favorable area for helium exploration, which has superior geological conditions for helium accumulation. The drilling results of helium exploration well indicate that the spatial distribution and mutual configuration relationship of the fault systems and favorable reservoir zones are the key to helium-rich gas accumulation. Clarifying the coupling relationship between Neogene tectonism and sedimentation will help to further ascertain the regularity of fault activity and characteristics of the spatial distribution of sedimentary facies of the study area, which is of great significance for clearing the exploration and deployment of helium resource. Combining with the various low-temperature thermochronology data accumulated of the adjacent area, this study conducts a comprehensive analysis of drilling logging, well logging, core samples, seismic, and carbon and helium isotope data. The results indicate that the multiple rapid uplift events of the Qinling orogenic belt aggravated the faulted effect and produced a series of secondary faults developed by deep major faults of the northern margin of Qinling Mountains, which can provide favorable migration channels for the upward migration of the deep helium and hydrocarbon carrier gas. The thick conglomerate layer of the lower Lantian-Bahe Formation is the sedimentary response of the rapid uplift of Qinling orogenic belt, and the Formation mainly developed the fan-delta root subfacies. The lithology of the upper Lantian-Bahe Formation is mainly characterized by the interbeds of sandstone, sandy mudstone, and mudstone, and the Formation mainly developed the middle and marginal sub-facies. Moreover, the carbon and helium isotope values of gas samples from Lantian-Bahe Formation indicate that coal-type methane gas is developed in this area and the helium is mainly the type of crustal source. Zhangjiapo Formation is mainly characterized by lacustrine facies, and the thin sandstone bodies in the Formation can be expected to be favorable facies zone for helium accumulation. The thick-bedded mudstone developed in the Zhangjiapo Formation is considered to be a favorable source rock segment of biogas and important cap in this area. Zhangjiapo Formation has a complete combination of generation, transport, storage, and cap for helium accumulation from bottom to top and can be used as an important zone for helium exploration.