The Yuntoujie W–Mo deposit is so far the only Indosinian granite-related deposit with an element association of W–Mo in the Nanling ore belt, South China. The granites in the Yuntoujie ore field consist of the Yuntoujie batholith and late-stage granites. The W–Mo mineralization is associated closely with the late-stage granites. Here we report major and trace element, Sr–Nd isotope and zircon Hf isotope compositions of the Yuntoujie batholith and the late-stage granites. The Yuntoujie batholith and the late-stage granites have high SiO2 (70.77–74.86wt.%) and alkaline (K2O+Na2O=6.27–8.27wt.%) concentrations and are characterized as peraluminous (A/CNK>1.1, A/NK=1.30–1.43). The Yuntoujie batholith and late-stage granites feature negative correlation between Th, Y and Rb, no positive correlation between P2O5 and SiO2 and high A/CNK values >1.1, suggesting that they could be classified as S-type granites. The Yuntoujie batholith and the late-stage granites might be sourced from the partial melting of Proterozoic crust without contribution from juvenile crust, as evidenced from the low 143Nd/144Nd values of 0.511942–0.512477, the ɛNd(t) values of −8.52 to −11.76 (falling in the field of Nd isotope evolution for the Proterozoic crust), and the zircon ɛHf(t) values of −7.19 to −14.89 with the TDM2 ranging from 1713Ma to 2187Ma. The major and trace element compositions of the Yuntoujie batholith and late-stage granites, especially the low CaO/Na2O and CaO/(MgO+FeOT) ratios and the high Rb/Ba and Rb/Sr ratios, further indicate that their sources are predominantly argillaceous sedimentary. The trace element characteristics, such as the positive correlation between La/Yb and La and between Ba and Sr and negative correlation between Ba and Rb, suggest that the late-stage granites are the product of highly fractionated melts of the Yuntoujie magma chamber. Moreover, 1) the ‘tetrad effect’ observed in the REE patterns for the late-stage tourmaline muscovite monzogranite porphyry and 2) the abundant fluid inclusions in their quartz phenocrysts imply that the processes of the volatile phase exsolution and the fluid-melt reaction had taken place in the evolved water-saturated magma. These geochemical features, together with the fact that the Yuntoujie magma chamber had survived for >10Myr, suggest that the peraluminous magma experienced a prolonged period of crystallization differentiation, which plays a key role in the formation of W–Mo mineralization associated with granites. From the observations that the granites in the Yuntoujie district were formed about 20–10Ma later than the peak age of the Indosinian collisions and that they all fall in the post-CEG area in the tectonomagmatic discrimination diagrams, we proposed that the Yuntoujie granites were formed in the post-collisional environment.