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The origin of giant rare earth element (REE)‐rich phosphorus deposits related to ultramafic rocks is unclear. To characterize the genetic linkage between ultramafic rocks and P–REE mineralization, we investigated the whole‐rock geochemistry, geochronology and Hf isotopic compositions, along with previously published data of barren and ore‐bearing clinopyroxenites from the giant Shangzhuang REE‐rich apatite deposit (containing about 51.1 million tonnes of P2O5 and 157,400 tonnes of REEs) in the Lajishan suture, Western China. The P–REE ores and barren biotite clinopyroxenites are composed predominantly of clinopyroxene and biotite, with high levels of apatite, amphibole, allanite, sulfide and oxide minerals in the ore‐bearing samples. Zircon and allanite U–Pb ages for the barren and ore‐bearing clinopyroxenites indicate they were formed between 467 and 465 Ma. The barren and ore‐bearing samples are characterized by high CaO and low SiO2 contents, as well as similar Hf isotope ratios (εHf[t]: +3.4 to +7.7), indicating that they represent an ultramafic magma system and have been derived from a similar source. They are enriched in light REEs and depleted in Nb–Ta–Zr–Hf–Ti, similar to arc‐related lavas found worldwide. The weakly evolved barren samples have high Ba/La, Rb/Y and Dy/Yb values, and their ages are coeval with calc‐alkaline granitic plutons in the belt, which postdate the formation of the Lajishan ophiolite by ~30 myr. This suggests that the primary magma originated from garnet peridotite mantle modified by subducted Proto‐Tethys oceanic crust‐derived fluids in an arc setting. The presence of apatite intergrowth with cumulus clinopyroxene without alteration features indicates that the deposit has a magmatic origin. The ore‐bearing clinopyroxenite contains higher contents of P, REEs, and high‐field‐strength elements than the barren clinopyroxenite, which could be attributed to the in situ accumulation of apatite and allanite in the residual magma. Thus, the formation of the P‐dominated orebodies results from phosphate saturation due to the extensive fractionation crystallization of clinopyroxene and biotite during magmatic evolution. REEs were primarily enriched in the late‐stage melt, which was compatible with apatite and allanite. We propose that the formation of the Shangzhuang REE‐rich apatite deposit can be attributed to a simple differentiation of ultramafic melts in an evolved magmatic system.