Vapor intrusion (VI) happens when volatile organic compounds (VOCs) migrate from subsurface sources into buildings, harming indoor air quality and occupants’ health. To investigate the migration and biodegradation of volatile organic compounds (VOCs) originating from subsurface sources, a soil column experiment was performed. In this experiment, high-concentration vapor from the liquid phase of toluene was steadily released into silty sand soil, aiming to simulate the conceptual model of a specific site. The experimental findings revealed that, within the silty sand soil, it took 36 h for toluene vapors to diffuse through a 120-cm-long soil column. During this process, the volume fractions of O₂ and CO₂ within the soil column varied. The level of microbial activity in the soil column first rose and then declined, as did the abundance of the dominant degrading toluene bacteria group. The experiment demonstrated that covering a certain thickness of silty sand soil could effectively retard the migration of toluene vapor. In addition, biodegradation occurred during the migration of the toluene vapor. However, long-term exposure to high-concentration toluene vapors inhibited both the activity and growth of microorganisms within the soil column.