The Yangla copper deposit is a rare Triassic intrusion-related Cu skarn system in the central part of the Jinshajiang tectonic belt, central Sanjiang orogenic belt, southwest China. Major- and trace-element compositions of apatites from ores, fertile calc-alkaline intrusions and its mafic microgranular enclaves, and barren calc-alkaline intrusions from the Yangla skarn copper deposit were measured by electron probe microanalysis and laser ablation–inductively coupled plasma–mass spectrometry. Results indicate that apatites grown within ores, fertile intrusions and its enclaves show similar features, but are different from that grown within barren intrusions. Apatite from fertile intrusions has higher Ca and correspondingly lower total trace-element contents, which partition onto the Ca sites, relative to that from barren intrusions. Apatites from the barren intrusions have high F and low Cl contents, and correspondingly high F/Cl ratios, which may have resulted from the assimilation of sediment. Apatites from fertile intrusions show relatively high Cl and low F contents, which may reflect crystallization from magmas with high water contents. Redox-sensitive elements in apatite can be used as indicators of the oxidation state of magmas. Apatites from the barren intrusion have lower V and As contents, higher Mn, Fe, and U contents, and more pronounced negative Eu anomalies than those from fertile intrusion, indicating that the barren magma was more reduced, consistent with its lower whole-rock Fe2O3/FeO and zircon Ce4+/Ce3+ ratios. These findings demonstrate that apatites are effective in distinguishing fertile from barren intrusions and can be used as a robust tool in mineral exploration.