The Longshoushan Metallogenic Belt (northwestern China) is known for its word-class Jinchuan Ni-Cu sulfide (Pt) deposit and is also an important uranium metallogenic belt. The Jiling uranium deposit in this belt is a typical Na-metasomatic uranium deposit, which rarely occurs in China. Mineralization in the Jiling uranium deposit is hosted in granitoids that have suffered a Na-metasomatic alteration. There are three kinds of uranium minerals, including uraninite, pitchblende, and coffinite in the Jiling uranium deposit. Pitchblende is the predominant uranium mineral. Integrating the mineralogy and geochemistry of uranium minerals, and in situ electron microprobe analyzer (EMPA) U-Th-Pb chemical dating, we aimed to unravel the age and nature of the mineralization, to decipher the characteristics of the hydrothermal alteration and the U mineralization process. Based on the microtextural features and compositional variations, primary uraninite was altered to uraninite A and B, and fresh pitchblende was altered to pitchblende A and B. The best-preserved uraninite crystals displayed a euhedral-shape with high Pb and low SiO2, CaO, FeO, and Al2O3 contents, and was interpreted as primary uraninite. The EMPA U-Th-Pb chemical ages revealed that uraninite may have formed at 435.9 ± 3.3 Ma. High ThO2 + ΣREE2O3 + Y2O3 contents illustrated that the best preserved uraninite crystallized at a high temperature. Altered pitchblende A showed a relatively brighter gray color in backscattered electron (BSE) images and with a lower SiO2 content than B. Three analysis spots of the fresh pitchblende showed low contents of ΣSiO2 + CaO, indicating no obvious alteration. EMPA U-Th-Pb chemical dating gave a mean chemical age of 361 Ma. The low Th + ΣREE2O3 contents indicated that this pitchblende formed at a relatively low temperature. According to the different characteristics of occurrence and chemical composition, the coffinite in the Jiling uranium deposit can be divided into coffinite A and B, respectively. The compositional variation of the fresh and altered uraninite and pitchblende indicated that both uraninite and pitchblende underwent at least two discrete hydrothermal fluid alterations. The U mineralization was divided into two stages; uraninite was formed at a high temperature and possibly from a magmatic-hydrothermal fluid during ore stage I. Then, pitchblende was formed at a low temperature, during ore stage II. According to the petrographic observations and their chemical compositions, coffinite A and B resulted from the alterations of uraninite and pitchblende, respectively.