Late Cretaceous granitoid-related deposits with different ore-forming elements show regional discrepancies: Sn polymetallic deposits formed in the southwestern margin of the Yangtze Block, whereas Cu-Mo deposits occurred in the neighbor Yidun arc. In order to figure out the controlling factors of this different mineralization, this study presents a combination of new zircon and apatite data with previously published geochemical data of Sn-related granitoids from Gejiu and Dachang deposits and Cu-Mo-related granitoids from Tongchanggou, Hongshan, and Relin deposits. The Sn-related granitoids are S-type granitoids with ɛNd(t) values of −10 to −7.6 and two-stage Nd model ages of 1700–1501 Ma, which implies that they were formed by partial melting of Proterozoic crustal materials. The Cu-Mo-related granitoids are I-type granitoids with adakitic features and wide ranges of εNd(t) values (−7.7 to −4.2) and zircon εHf(t) values (−9.6 to −1.3), reflecting the contributions of crustal- and mantle-derived materials in the source. Compared with the Cu-Mo-related granitoids, higher whole-rock SiO2 contents and Rb/Sr ratios, lower Nb/Ta, Zr/Hf, and K/Rb ratios in the Sn-related granitoids together with variations in zircon and apatite trace element ratios affirm that they are more fractionated. The magmas of Cu-Mo-related granitoids however are more oxidized and hydrous. They show higher zircon EuN/EuN* (average = 0.70), Ce4+/Ce3+ (average = 671), Ce/√(Ui×Ti) ratios and apatite EuN/EuN*ratios, and lower Ti-in-zircon temperature (average = 675) and zircon (Ce/Nd)/Y ratios than those of the Sn-related granitoids (average zircon EuN/EuN* = 0.09, average Ce4+/Ce3+ ratios = 53, average Ti-in-zircon temperature = 749). The higher Cl content in apatite for the Cu-Mo-related granitoids reflects a Cl-richer magma for the Cu-Mo-related granitoids. Combined with the previous studies on regional contemporaneous magmatic activity and structures, the Sn- and Cu-Mo-related granitoids formed in the intraplate and post-collisional extension environments, respectively. Reduced and fractionated crustal-derived magmas facilitate Sn enrichment, while oxidized, hydrous, and Cl-rich magmas with mantle-derived materials promote Cu-Mo mineralization. Accordingly, magma source, fractionation, redox, and volatile conjunctively control the formation of granitoid-related deposits with different ore element assemblages.