High-resolution microanalysis was performed on conodonts collected from the Huanghuachang section in the Yichang area using laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS). This region is regarded as a standard section for the division and correlation of the Ordovician system in southern China. The results show that the values of (La/Yb)N and (La/Sm)N decrease, while the values of δCe increase as seawater deepens and energy decreases. As the sedimentary environment changes from shallow-water carbonate platform to platform margin to open continental shelf to shelf basin, rare earth element distribution curves gradually transform from a right inclined pattern to a flat pattern to a left inclined pattern and a hat-shaped pattern. The present work proves that the values and distributive patterns of rare earth elements in conodonts correspond with the sedimentary environment, and therefore provide reliable evidence for the application of rare earth element concentrations of biogenic phosphates such as conodonts for palaeoenvironmental reconstructions.