The Yuhaixi Mo(Cu) deposit is a new discovery in the eastern section of the Dananhu-Tousuquan island arc, Eastern Tianshan. However, the genesis of the Yuhaixi Mo(Cu) deposit is still not fully understood. The Yuhaixi intrusion is composed of monzonitic granites, diorites, granites, and gabbro dikes, among which disseminated or veinlet Mo and Cu mineralization is mainly hosted by the monzonitic granites. The LA-ICP-MS zircon U-Pb dating yields emplacement ages of 359.4 ± 1.6 Ma for the monzonitic granite, 298.8 ± 1.8 Ma for the diorite, and 307.0 ± 2.3 Ma for the granite. The Re-Os dating of molybdenite hosted by monzonitic granite yields a well-constrained 187Re-187Os isochron age of 354.1 ± 6.8 Ma (MSWD = 1.7) with a weighted average age of 344.5 ± 3.1 Ma. The Mo mineralization is closely associated with the Yuhaixi monzonitic granite. The Yuhaixi monzonitic granite rocks are characterized by high silica (SiO2 > 70 wt.%), low MgO (0.23–0.36), Ni, Cr contents, and they are enriched in light rare earth elements (LREEs) and large ion lithophile elements (LILEs: e.g., K, Ba, Pb and Sr), and depleted in heavy rare earth elements (HREEs) and high field-strength elements (HFSEs: e.g., Nb, Ta and Ti). They are weak peraluminous and have high εHf(t) (11.37–17.59) and εNd(t) (1.36–7.75) values, and varied initial 87Sr/86Sr (0.7037–0.7128) values. The Yuhaixi post-ore granites exhibit similar geochemical and isotopic signatures to the Yuhaixi monzonitic granite. These characteristics suggest that the Yuhaixi felsic rocks are likely sourced from the partial melting of the juvenile lower crust. The Yuhaixi diorite has low SiO2, and K2O contents, relatively high Na2O, MgO (Mg# = 45–53) contents, and depletions in HFSE (e.g., Nb, Ta, and Ti). These geochemical features, coupled with isotopic data such as low initial 87Sr/86Sr (≤0.7043), high εNd(t) (2.5 to 3.0) and εHf(t) (≥11.6) values, and young Hf model ages, suggest that their parental magmas possibly originated from the partial melting of the depleted lithospheric mantle that was metasomatized by hydrous melts or fluids from the subducting oceanic plate. Integrating our new results with previous works on the Dananhu-Tousuquan island arc belt, we suggest that the Yuhaixi Mo(Cu)deposit is likely sourced from the juvenile lower crust, which was formed in an arc setting, where the bipolar subduction of the North Tianshan oceanic slab forms the Dananhu Tousuquan belt to the north and the Aqishan-Yamansu belt to the south. The eastern section of the Dananhu-Tousuquan island arc is a promising target for late Paleozoic porphyry Mo(Cu) deposits.