Southern blight caused by Sclerotium rolfsii (S. rolfsii) represents a significant threat to the medicinal plant Atractylodes macrocephala Koidz. (A. macrocephala), with effective control measures remaining limited. Chrysanthemum indicum polysaccharides (CIP) have been identified as an elicitor capable of inducing defense responses in A. macrocephala against S. rolfsii infection. However, the molecular mechanisms underlying CIP recognition remain poorly understood. In this study, comparative transcriptome analysis revealed two potential LysM-receptor kinases, AmCERK1 and AmLYK3, as candidate receptors for CIP recognition. These genes, which are orthologous to Arabidopsis CERK1 and Medicago truncatula LYK3, exhibited significant up-regulation upon CIP treatment. Bimolecular fluorescence complementation (BiFC) assays demonstrated that AmCERK1 and AmLYK3 interact in a CIP-dependent manner. Transient overexpression experiments further confirmed that CIP treatment markedly enhanced the expression of these receptor genes. Virus-induced gene silencing (VIGS) assays indicated that CIP treatment could partially compensate for the suppression of AmCERK1 and AmLYK3, highlighting their critical role in CIP-induced defense responses. Collectively, these findings suggest that AmCERK1 and AmLYK3 form a pattern recognition receptor (PRR) complex essential for CIP perception, potentially facilitating pattern-triggered immunity (PTI) in A. macrocephala. These findings reveal a novel receptor recognition complex comprising AmCERK1 and AmLYK3, offering crucial insights into the mechanisms of innate immune recognition in plants.