Lentinula edodes (L. edodes) is a significant edible and medicinal mushroom with essential nutrient elements for its growth, including Fe²⁺, K⁺, and Mn²⁺. However, the molecular mechanisms by which these metal ions regulate the mycelial growth of L. edodes have been poorly elucidated at the transcriptomic level. In this study, plate culture was performed using concentration gradients to screen for optimal concentrations. Transcriptome sequencing (RNA‑seq) and qRT‑PCR validation were performed to elucidate the regulatory effects and molecular mechanisms of the three metal ions on the mycelial growth of L. edodes. The results showed that Fe²⁺ at concentrations above 20 µg/mL significantly inhibited mycelial growth; K⁺ at 1200 µg/mL and Mn²⁺ at 50 µg/mL significantly promoted mycelial growth, with increases of 21.22% and 10.77%, respectively. Transcriptomic analysis revealed that Fe²⁺ primarily induced abnormal protein folding and suppressed material and energy metabolism, thus inhibiting mycelial growth. Mycelial growth is promoted by K⁺ by enhancing detoxification and secondary metabolism and by activating mitochondrial function and the oxidative phosphorylation pathway. The proliferation and growth of mycelial cells are regulated by Mn²⁺ through mechanisms that govern DNA repair and recombination, cell cycle progression, and detoxification. This study elucidates the differential regulatory mechanisms of the three metal ions on the mycelial growth of L. edodes at the transcriptomic level, offering a rationale for enhancing mineral nutrition and high‑yield cultivation of L. edodes.