Ganoderma lucidum is a medicinal fungus widely utilized in traditional medicine and functional foods. Its primary bioactive constituents are ganoderic acids (GAs), a group of triterpenoid compounds. While chemical-induced apoptosis has previously been shown to enhance GAs production, this study investigates the role of physical stress in this regulatory pathway. We demonstrate that heat-induced apoptosis significantly increases GAs production in G. lucidum. To determine whether apoptosis directly regulates this process, we overexpressed the human anti-apoptotic gene Bcl-2 in G. lucidum, confirming expression via RT-PCR and Western blot analysis. Upon heat-induced apoptosis, these Bcl-2 overexpression mutants exhibited increased mycelial cell viability, accompanied by reduced metacaspase activity and, notably, decreased GAs production. Furthermore, we identified a Type I metacaspase gene in G. lucidum, Glmca1, which contains highly conserved catalytic domains common across fungal species. Silencing of Glmca1 followed by heat-induced apoptosis led to results similar to Bcl-2 overexpression: enhanced cell viability, suppressed metacaspase activity, and a significant reduction in GAs yield. These findings provide compelling evidence that apoptosis functions as a critical regulatory mechanism for secondary metabolite production in G. lucidum. Consequently, modulating apoptotic pathways through physical induction offers a promising strategy for enhancing the production of bioactive ingredients in medicinal fungi.