The Sclerotium rolfsii-induced Southern blight poses a severe threat to the medicinal plant Atractylodes macrocephala Koidz (Atractylodes), yet effective control strategies for this pathogen remain limited. Chrysanthemum indicum polysaccharides (CIP) as an elicitor have been verified to induce the defense response of Atractylodes against Sclerotium rolfsii. However, the fundamental mechanisms underlying ligand perception remain largely elusive. In this study, a comparative transcriptome analysis was conducted to identify two potential LysM-receptor kinases in Atractylodes, namely AmCERK1 and AmLYK3, as pattern recognition receptor (PRR) complexes recognize CIP. Subsequently, the involvement of these genes in CIP-induced defense responses was further confirmed. Notably, AmCERK1 and AmLYK3 are orthologs of Arabidopsis CERK1 and Medicago truncatula LYK3 respectively, exhibiting up-regulation upon CIP treatment. The BiFC assays demonstrate that the interaction between these two receptors necessitates the presence of CIP. Transient overexpression experiments reveal that CIP treatment enhances the expression of the receptor gene in the plants significantly. Additionally, the CIP treatment effectively mitigated the inhibition of target genes during the silencing of AmCERK1 and AmLYK3 in seedlings induced by pTRV-based VIGS application. The CIP is required for the interaction of AmCERK1 and AmLYK3 and facilitating the establishment of PTI in Atractylodes. This is novel receptor recognition complexes, and is crucial to probe into mechanisms of innate immune recognition in plant.