The damage caused by petroleum hydrocarbon pollution to soil and groundwater environment is becoming increasingly significant. The vadose zone is the only way for petroleum hydrocarbon pollutants to leak from surface into groundwater. The spatial distribution characteristics of indigenous microorganisms in vadose zone, considering presence of capillary zones, have rarely been reported. To explore the spatial distribution characteristics of indigenous microorganisms in vadose zone contaminated by petroleum hydrocarbons, a one-dimensional column migration experiment was conducted using n-hexadecane as characteristic pollutant. Soil samples were collected periodically from different heights during experiment. Corresponding environmental factors were monitored online. The microbial community structure and spatial distribution characteristics of the cumulative relative abundance were systematically analyzed using 16S rRNA sequencing. In addition, the microbial degradation mechanism of n-hexadecane was analyzed using metabolomics. The results showed that presence of capillary zone had a strong retarding effect on n-hexadecane infiltration. Leaked pollutants were mainly concentrated in areas with strong capillary action. Infiltration and displacement of NAPL-phase pollutants were major driving force for change in moisture content (θ) and electric conductivity (EC) in vadose zone. The degradation by microorganisms results in a downward trend in potential of hydrogen (pH) and oxidation-reduction potential (ORP). Five petroleum hydrocarbon-degrading bacterial phyla and 11 degradable straight-chain alkane bacterial genera were detected. Microbial degradation was strong in the area near edge of capillary zone and locations of pollutant accumulation. Mainly Sphingomonas and Nocardioides bacteria were involved in microbial degradation of n-hexadecane. Single-end oxidation involved microbial degradation of n-hexadecane (C16H34). The oxygen consumed, hexadecanoic acid (C16H32O2) produced during this process, and release of hydrogen ions (H+) were the driving factors for reduction of ORP and pH. The vadose zone in this study considered presence of capillary zone, which was more in line with actual contaminated site conditions compared with previous studies. This study systematically elucidated vertical distribution characteristics of petroleum hydrocarbon pollutants and spatiotemporal variation characteristics of indigenous microorganisms in vadose zone considered presence of capillary zone. In addition, the n-hexadecane degradation mechanism was elucidated using metabolomics. This study provides theoretical support for development of natural attenuation remediation measures for petroleum-hydrocarbon-contaminated soil and groundwater.