The genetic links between skarn deposits and their causative intrusions are often difficult to establish with in situ dating techniques since ultra-high temporal resolution is required (i.e., < 0.1%). Strontium isotope can be applied to further test their causality, because of its sensitivity to water-rock interaction and country-rock contamination. Here we demonstrated the effectiveness of this approach using two skarn deposits (Zhibula and Anqing) as an example. While in situ garnet/zircon U-Pb dating indicates contemporary intrusions for both deposits, but the genetic links between mineralization and intrusions are contested owing to the limited temporal resolution. We further tested these apparent genetic links via in situ Sr isotope discrimination between mineralization-related epidote and igneous apatite from hypothesized causative intrusions. For Zhibula, the U-Pb ages of garnet (17.0 ± 0.4 Ma) and zircon (16.9 ± 0.3 Ma) support an apparent genetic link between Cu mineralization and the Zhibula granodiorite. This observation has been further supported by the 87Sr/86Sr ratio of hydrothermal epidote (0.70657 ± 0.00025), which can be interpreted by binary mixing between the granodiorite (0.71136 ± 0.00253) and the wall rock (Yeba formation; 0.70456 ± 0.00118). For Anqing, the U-Pb ages of garnet (138.1 ± 1.9 Ma) and zircon (137.1 ± 1.3 Ma) also support an apparent genetic link between Cu-(Fe-Au) mineralization and the Yueshan diorite. However, the 87Sr/86Sr ratio (0.71468 ± 0.00356) of hydrothermal epidote is too radiogenic to be explained by mixing between the Yueshan diorite (0.70654 ± 0.00012) and the Triassic carbonates (0.70810 ± 0.00015), which implies the presence of an unknown or unexposed causative intrusion. Our study highlights the risk of solely relying on in situ radiometric dating to establish genetic links between mineralization and spatial-related intrusions. Instead, integrating Sr isotopic fingerprinting with geochronology and deposit geology could be more informative.