The Xiaotuergen Cu deposit is the first Cu deposit described in the Northern Chinese Altai Orogen, Xinjiang, NW China. The multiple phases of granitic intrusions occur in the Xiaotuergen region, including the intrusions of granodiorite porphyry, granite porphyry, and biotite monzogranite. Among these types of intrusions, Cu mineralization is considered to be closely related to the early Hercynian granodiorite porphyry. However, the precise emplacement ages, petrogenesis, redox states, and tectonic setting of the three Xiaotuergen granitoids and the relationship between these granitoids and mineralization was unclear. To resolve these issues, zircon U–Pb dates, zircon in situ trace element concentrations, Hf isotopic compositions, apatite in situ major element concentrations, and whole-rock geochemistry were determined in this study. Three different intrusive phases are recognized within the district; in order of deceasing age, these phases are biotite monzogranite, granodiorite porphyry, and granite porphyry, which have the ages of 400.2 ± 1.6 Ma to 399.6 ± 2.4 Ma, 390.3 ± 1.6 Ma to 377.1 ± 1.6 Ma, 381.0 ± 2.0 Ma to 378.7 ± 1.2 Ma, respectively, suggesting that they were emplaced during the Early-Middle Devonian. Geochemical data show that these intrusions are metaluminous to weakly peraluminous (A/CNK = 0.91–1.28), calc-alkalic to shoshonitic I-type granitoids. The two Harker plot trends reveal derivation from two magma sources (biotite monzogranite vs granodiorite porphyry and granite porphyry) that experienced different evolutionary processes. Multiple indicators, including the zircon Ce4+/Ce3+ ratio and oxygen fugacity (logfO2) values, apatite Mn oxybarometer, and whole-rock Fe2O3/FeO ratio, consistently indicate that the parental magma of the fertile granodiorite porphyry was more oxidized than that of the two barren intrusions (biotite monzogranite and granite porphyry). Furthermore, apatite grains from the fertile granodiorite porphyry have higher Cl contents and Cl/F ratios than those of the ore-barren biotite monzogranite and granite porphyry, which may have resulted from the higher water content of the parental magma and increased lithospheric mantle-derived fluid involvement in their generation. Thus, higher Cl/F ratios of apatite can be used to discriminate fertile granitoid intrusions that host Cu mineralization in the Northern Altai orogen. Zircon Hf isotopic compositions show widely ranging and mostly positive εHf (t) values (−4.2 to +11.4, mainly concentrated between +2 and +8). These isotope characteristics in combination with young zircon TDMC (Hf) ages (655–1,659 Ma; mainly concentrated between 850 Ma and 1250 Ma) indicate that the Xiaotuergen granitoids were most likely derived from the partial melting of juvenile lower crust, with some interaction of mantle materials from the underlying mantle wedge. The three Xiaotuergen granitoids were enriched in light rare earth elements and large ion lithophile elements, depleted in heavy rare earth elements, and showed negative Nb, Ta, Sr, P, and Ti anomalies, displaying typical arc geochemical affinities. Combined with the regional tectonic evolution, we propose that the Xiaotuergen granitoids were generated in a continental arc setting associated with subduction processes, which were the products of syn-accretion orogenic processes.