In Hainan field-grown Curcuma wenyujin plants, wilting and root rot symptoms were observed. A root-lesion nematode, Pratylenchus sp., was detected in the rhizosphere soil of diseased plants. To determine the this nematode species and its role as the causal agent of C. wenyujin wilting and root rot, the nematode associated with C. wenyujin roots was identified through integrated morphological and molecular biological methods. And following Koch’s postulates, the pathogenicity of this nematode was confirmed via greenhouse pot inoculation experiments. The results demonstrated that the nematode was Pratylenchus coffeae. This nematode infested the root tissues of C. wenyujin, leading to browning, necrosis, or rotting of roots and rhizomes, accompanied by plant stunting, yellowing, and wilting, leading to significant reductions in rhizome yield and quality. This study confirms P. coffeae as the pathogen responsible for wilting and root rot in C. wenyujin. This is the first discovery and confirmation of P. coffeae infecting and damaging the medicinal plant C. wenyujin, and causing root rot nematode disease. These findings provide critical insights for the diagnosis and management of this disease.