Intersection-type uranium deposits refer to the uranium deposits that are located at the intersection of mafic dykes and silicified faults and are an important type of granite-related uranium deposits in South China. However, the genesis of these deposits still remain poorly understood. The Egongtang uranium deposit is a typical intersection-type uranium deposit in the Huangsha uranium ore district (southern Jiangxi) that bears a number of NWW-trending mafic dykes, thus providing an excellent opportunity to study the genesis of intersection-type uranium deposits. In this study, the mineralization age and genesis of this deposit were constrained using in situ zircon and pitchblende U-Pb geochronology, whole-rock geochemistry, and pyrite sulfur isotope data. The zircon U-Pb dating constrains the crystallization ages of 240.4 ± 1.3 Ma and 160.7 ± 1.6 Ma for granites in the Huangsha ore district. The samples (including altered and unaltered) of the granites are characterized by variable whole-rock U contents of 5.8–14.1 ppm and Th/U ratios of 2.4–7.7, which favor the crystallization of uraninite in the granites and suggest U leaching from the granites during alteration. In situ U-Pb dating on pitchblende from the Egongtang uranium deposit yielded a lower intercept age of 89.8 ± 1.1 Ma, indicating that the uranium mineralization took place at the Late Cretaceous. Pyrite associated with pitchblende has δ34S values ranging from 1.6‰ to 3.8‰, suggesting a magmatic source. This study indicates that granites in this area might have represented the source of uranium for the Egongtang deposit, and that the uranium mineralization was probably related to the Late Cretaceous crustal extension in South China.