The Qin-Fang Trough, South China, trends northeast-southwest, orthogonal to the adjoining southern margin of the craton. The Devonian strata within the trough are unconformable on late Neoproterozoic units of the Yunkai Massif, indicating that strata within the trough are autochthonous. U-Pb ages and Hf isotope compositions of detrital zircons from the Silurian to Devonian succession are consistent with derivation from the massif. In comparisons of our data with those frome quivalent units in the Ailaoshan Belt and Hainan Island, detrital zircons from the Silurian strata show similar age distributions and Hf isotope compositions, indicating that the three areas shared a common source and were adjacent to each other during the Silurian. In contrast, the age distributions of detrital zircons preserved in Devonian strata in the Qin-Fang area are different from those of equivalent units in the Ailaoshan Belt. This, along with the absence of Devonian strata on Hainan Island, suggests that the Qin-Fang area had separated from the Ailaoshan Belt by the Devonian. This change is linked to opening of the Ailaoshan Ocean, which was synchronous with expansion of the Qin-Fang Trough and the adjoining Youjiang Basin into epicontinental basins during the Devonian and Carboniferous. Combining these findings with temporal and spatial correlations, we conclude that the Qin-Fang Trough originated as an aulacogen: a “failed” rift of a three-armed rift system, with the other two rift arms evolving into the Ailaoshan Ocean during the opening of Paleo-Tethys. The Ailaoshan Ocean was an Atlantic-type oceanic basin with rifting commencing in the Early Silurian.