Phosphorites (P₂O₅ content > 18 wt%) are widespread in the world; however, high-quality phosphorite (P₂O₅ content > 30 wt%) is exceptionally rare. In South China, the Devonian Shifang phosphorite deposit represents not only a high-quality phosphorus ore resource but also hosts abundant rare earth elements (up to 3677.6 ppm). Despite its significance, the provenance of this unique phosphorite deposit has remained unclear. In this study, we conducted U-Pb dating, Hf isotope, and trace element concentrations analysis of detrital zircon from the phosphorite in the Shifang phosphorite deposit to well constrain the specific provenance and potential material source of the phosphorite. Cathodoluminescence (CL) images and trace elements analysis of zircons suggested that the majority of zircons have a magmatic origin. The U-Pb dating age of these zircons revealed three main age peaks at ∼ 560–520 Ma, ∼850–750 Ma and ∼ 1050–950 Ma. A comparison of the εHf values of zircons for the same age group worldwide revealed the following: (1) The 1050 ∼ 950 Ma detrital zircon in the Shifang phosphorite deposit could be derived from North India; (2) The 850–750 Ma zircons originated from Tonian granites in the western South China Block; (3) The 560–520 Ma zircons had two sources, one could be the Kuungan orogeny in the east-Gondwana, and another could be the Arabian-Nubian Shield in the northern-west-Gondwana. In addition, our new age histograms of detrital zircon U-Pb ages are well consistent with underlying strata, such as Silurian and early-middle Devonian. Combining these findings with the geological activities in the study area, we conclude that zircons in the Shifang phosphorite deposit may directly originate from the underlying strata in the study area and the Cambrian Qingping phosphorite deposit may have served as an essential phosphorus source for the Shifang phosphorite deposit.