To enhance the regulatory network of the Zn2Cys6-type transcription factor, PdTP1, this study employed transcriptome sequencing technology to screen for genes related to the biotransformation of limonene into α-terpineol by Penicillium digitatum DSM 62840 and the regulation of fungal growth. Transcriptome sequencing was performed on the wild-type P. digitatum DSM 62840 and PdTP1-silenced strains to investigate the metabolic pathways and biological functions of key differentially expressed genes (DEGs). Reliability of the transcriptome sequencing results was verified through quantitative real-time PCR. A total of 1 221 DEGs, including 499 upregulated and 722 downregulated genes, were identified. GO and KEGG analyses indicated that these DEGs were significantly enriched in the metabolism and biosynthesis of various substances, including sugars, amino acids, and fatty acids. Among them, the expression of certain genes related to terpene metabolism or synthesis, fungal growth, and the stress response were significantly regulated by PdTP1, suggesting that these genes may play important roles in regulating the biotransformation of limonene to α-terpineol and the growth of P. digitatum. Reliability of the transcriptome sequencing results was confirmed by the quantitative real-time PCR results. In summary, this study refined the regulatory network of the transcription factor, PdTP1, by examining variations in gene transcription regulated by it, providing evidence for elucidating the molecular mechanisms by which PdTP1 regulates α-terpineol biosynthesis and fungal growth.