Penicillium griseofulvum CF3 is a fungus isolated from healthy strawberry soil, with the potential to promote the growth of plants and enhance their resistance to diseases. However, the genome sequence of P. griseofulvum CF3 remains unclear. Therefore, we performed the whole-genome CCS sequencing of P. griseofulvum CF3 using the PacBio Sequel II platform. The assembled genome comprised 104 contigs, with a total length of 37,564,657 bp, encoding 13,252 protein-coding genes. Comprehensive functional annotation was performed using various BLAST databases, including the non-redundant (Nr) protein sequence database, Gene Ontology (GO), the Kyoto Encyclopedia of Genes and Genomes (KEGG), EuKaryotic Orthologous Groups (KOG), and the Carbohydrate-Active enZymes (CAZy) database, to identify and predict protein-coding genes, tRNAs, and rRNAs. The Antibiotics and Secondary Metabolites Analysis Shell (Antismash) analysis identified 50 biosynthetic gene clusters involved in secondary metabolite production within the P. griseofulvum CF3 genome. The whole-genome sequencing of P. griseofulvum CF3 helps us to understand its potential mechanisms in promoting plant growth and enhancing disease resistance, paving the way for the application of the CF3 strain in sustainable crop production.