Exposure to ambient fine particulate matter (PM) in transit microenvironments (TMEs), which mainly comes from traffic emissions, is associated with various adverse health effects. Many studies have investigated the exposure levels and health risk to commuters in TMEs; however, the application of spatial techniques has been limited to a handful of in-transit studies, and information on spatiotemporal variations of in-transit particle concentrations remains sparse. This study aims to examine spatiotemporal variations of in-cabin particle concentrations in transit and the correlations between en-route environmental factors and the variations of particle concentrations in transit. To this end, we propose a portable monitoring system for measuring the particle concentrations and corresponding travel conditions on public transit trips. The measurements were performed during peak hours of both bus and metro services in Shenzhen China. Our results highlight that temporal variations of particle concentrations exist between different trips during the same peak hours. The particle concentrations are higher on the start/end segments of the routes than on any other segment. The variations in particle concentrations on different route segments are significantly correlated with travel conditions (p < 0.01 and p < 0.05) and urban ambient conditions (p < 0.01). Moreover, opposite effects of ventilation, wind speed, and the posture of the investigators on the variations of particle concentrations on different segments are identified between bus and metro. In addition, passengers are exposed to higher particle concentrations on longer trips. Utilizing our methodology and results, policy makers and other researchers may further explore the exposure to particle pollution on public transit.