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.