BackgroundChrysanthemum Fusarium wilt is a common fungal disease caused byFusarium oxysporum, which causes continuous cropping obstacles and huge losses to the chrysanthemum industry. The defense mechanism of chrysanthemum againstF. oxysporumremains unclear, especially during the early stages of the disease. Therefore, in the present study, we analyzed chrysanthemum ‘Jinba’ samples inoculated withF. oxysporumat 0, 3, and 72 h using RNA-seq.ResultsThe results revealed that 7985 differentially expressed genes (DEGs) were co-expressed at 3 and 72 h afterF. oxysporuminfection. We analyzed the identified DEGs using Kyoto Encyclopedia of Genes and Genomes and Gene Ontology. The DEGs were primarily enriched in “Plant pathogen interaction”, “MAPK signaling pathway”, “Starch and sucrose metabolism”, and “Biosynthesis of secondary metabolites”. Genes related to the synthesis of secondary metabolites were upregulated in chrysanthemum early during the inoculation period. Furthermore, peroxidase, polyphenol oxidase, and phenylalanine ammonia-lyase enzymes were consistently produced to accumulate large amounts of phenolic compounds to resistF. oxysporuminfection. Additionally, genes related to the proline metabolic pathway were upregulated, and proline levels accumulated within 72 h, regulating osmotic balance in chrysanthemum. Notably, the soluble sugar content in chrysanthemum decreased early during the inoculation period; we speculate that this is a self-protective mechanism of chrysanthemums for inhibiting fungal reproduction by reducing the sugar content in vivo. In the meantime, we screened for transcription factors that respond toF. oxysporumat an early stage and analyzed the relationship betweenWRKYand DEGs in the “Plant-pathogen interaction” pathway. We screened a keyWRKYas a research target for subsequent experiments.ConclusionThis study revealed the relevant physiological responses and gene expression changes in chrysanthemum in response toF. oxysporuminfection, and provided a relevant candidate gene pool for subsequent studies on chrysanthemum Fusarium wilt.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12870-023-04331-7.