In recent years, magnetic fields have emerged as a non-thermophysical treatment with a significant impact on microbial fermentation processes. Brassica trispora is a microorganism known for its industrial-scale production of lycopene and high yield of single cells. This study aimed to investigate the impact of low-frequency magnetic fields on lycopene synthesis by Brassica trispora and elucidate the underlying mechanism for enhancing lycopene yield. The results indicate that both the intensity and duration of the magnetic field treatment influenced the cells. Exposing the cells to a 0.5 mT magnetic field for 48 h on the second day of fermentation resulted in a lycopene yield of 25.36 mg/g, representing a remarkable increase of 244.6% compared to the control group. Transcriptome analysis revealed that the alternating magnetic field significantly upregulated genes related to ROS and the cell membrane structure, leading to a substantial increase in lycopene production. Scanning electron microscopy revealed that the magnetic field treatment resulted in a rough, loose, and wrinkled surface morphology of the mycelium, along with a few micropores, thereby altering the cell membrane permeability to some extent. Moreover, there was a significant increase in intracellular ROS content, cell membrane permeability, key enzyme activity involved in lycopene metabolism, and ROS-related enzyme activity. In conclusion, the alternating frequency magnetic field can activate a self-protective mechanism that enhances lycopene synthesis by modulating intracellular ROS content and the cell membrane structure. These findings not only deepen our understanding of the impact of magnetic fields on microbial growth and metabolism but also provide valuable insights for developing innovative approaches to enhance carotenoid fermentation.