Research on the migration and transformation of phenol with space and temporal variability in the vadose zone is hindered by monitoring technology in field experiments. Four column experiments were conducted to investigate the effect of porous media size, volatilization, biological effects, and oxidation on the transport of phenol in the vadose zone. The initial inflow phenol concentration of each column was 500 mg/L, and the final outflow concentrations were 0, 348, 240, and 365 mg/L, More than 90% of reduction of phenol concentration occurred at the top of the simulation column. Results show that volatilization and oxidation are the main factors that could lead to the decrease of phenol concentration in an open system. However, these two processes cannot be accurately separated. The migration rate of phenol was larger in coarse sands (6.06 cm/d) than in fine sands (4.55 cm/d). Phenol biodegradation did not occur under experimental conditions. However, mercury (as biological inhibitor) could react with phenol to generate a mercury–phenol complex, which could lead to the reduction of phenol concentration to 21.6% in the simulation experiment.