Compared with conventional microbial hosts, filamentous fungi have distinct advantages for the industrial-scale biosynthesis of high-value chemical compounds. However, current research on strain engineering and fermentation optimization strategies for synthetic biology applications is limited in filamentous fungi, especially in industrial production strains. In this study, we established a CRISPR/Cas9-based gene editing system in Botrytis cinerea strain TB-31, an important filamentous fungal platform for the study of the biosynthesis and regulation of the sesquiterpenoid abscisic acid (ABA). This system enables efficient single- and multigene knockout, large-fragment deletion, and heterologous protein expression. Among the engineered mutant strains, the △bcaba1234 strain with complete ablation of the ABA biosynthetic gene cluster (BGC) demonstrated significant metabolic flux rewiring, redirecting cellular resources toward terpenoid precursor biosynthesis; this metabolic reprogramming proves pivotal for high-value terpenoid biosynthesis. This study not only establishes an efficient genome editing tool for the ABA-producing strain B. cinerea TB-31 but also provides a foundation for its development as a new potential terpenoid-producing chassis strain.