The Qinzhou Bay-Hangzhou Bay Suture Zone (QHSZ) lies between the northwestern Yangtze Block and the southeastern Cathaysia Block in South China. An integrated zircon U-Pb age, whole-rock and mineral geochemical analyses have been enabled for understanding the Neoproterozoic and early Paleozoic geological evolution of the QHSZ. Zircon U-Pb dating reveals that the Guizi metabasite and Zhuya gabbro were formed at 948 ± 11 Ma and 450.8 ± 2.9 Ma, respectively. The Guizi metabasites are characterized by Nb enrichments (8.18–16.11 ppm) with high Nb/La (0.76–0.98) and Nb/U (17.86–25.65) ratios. The samples are also LREE/HREE ([La/Yb]N = 2.66–3.29) and LILEs (Rb, Th, U and Pb) enriched with weakly depleted HFSEs (Nb, P and Ti), resembling the Nb-enriched basalts. These geochemical signatures were likely to be originated from a newly subducted slab. Elemental contrasts illustrate that the Guizi metabasites are geochemically consistent with the Neoproterozoic Nb-enriched basalts along the Wuyi-Yunkai Domain, South China. Age and elemental characteristics of the Guizi samples suggest an earliest Neoproterozoic subduction within the QHSZ. The Zhuya gabbro samples have high contents of MgO (11.23–14.48%), Cr (520.8–782.7 ppm) and Ni (126.1–203.7 ppm), (La/Yb)N = 1.89–2.41, Eu/Eu* = 0.84–0.90, positive LILEs (Rb, Th, Sr and Pb) anomalies and negative HFSEs (Nb, P and Ti) anomalies. Clinopyroxene geochemical data show a significant arc cumulates trend. They were considered to be derived from an E-MORB-like source modified by subduction-related fluids. Geochemical modelling indicates that a mixture of the Neoproterozoic mafic magma and SCB sediments (20–40%) can match the elemental and Sm-Nd isotopic compositions of the Zhuya gabbros, which suggests the involvement of Neoproterozoic subduction-modified mantle. Combined with regional geological and geochemical data, it is concluded that the Yangtze and Cathaysia blocks were likely sutured along the QHSZ forming an earliest Neoproterozoic arc-back-arc system, and the early Paleozoic mafic rocks are dominantly remelting products of the Neoproterozoic subduction modified mantle.