The rutile and apatite U-Pb dating is one of the important methods in the study of diagenetic geochronology. However, there is often a phenomenon of inconsistency or decoupling between the U-Pb timing of rutile and apatite and zircon in the same rocks. It has caused the problems to effectively constraint the formation timing of rocks, especially in the region with multi-stage magmatism. In this study, the rutile and apatite U-Pb ages for the Anglonggangri amphibolite and granodiorite were dated. These ages also have large derivations from the corresponding zircon U-Pb ages. Based on previous studies on the granites developed in the Anglonggangri area, as well as the timing of magmatism in the neighboring areas of Zuozuo-Xiongba, this study analyzes the reasons for the inconsistent U-Pb ages between rutile and apatite and zircon. It is believed that the regionally widespread multi-stage magmatic activities have led to the reset of the U-Pb closed system of rutile and apatite in the Anglonggangri amphibolite and granodiorite. The U-Pb ages recorded by rutile and apatite reflect magmatism of the Late Cretaceous-Early Paleocene, Eocene, and Oligocene-Miocene, respectively. When using the rutile and apatite U-Pb ages to determine the timing of their hosted rocks in the areas with multi-stage magmatism, someone should be cautious and should carefully evaluate the real geological significances on the rutile and apatite U-Pb isotopic systems.