Due to rapid economic development in recent years, China has become a major global source of refractory black carbon (rBC) particles. However, surface rBC measurements have been limited, and the lower troposphere suffers from a complete lack of measurements, especially in heavily rBC-polluted regions such as China’s capital, Beijing (BJ). In this study, we present the first concentration measurements using an airborne Single Particle Soot Photometer (SP2) instrument, including vertical distributions, size distributions, and the mixing state of rBC particles in the lower troposphere in BJ and its surrounding areas. The measurements were conducted from April to June 2012 during 11 flights. The results show that the vertical rBC distributions had noticeable differences between different air masses. When an air mass originated from the south of BJ (polluted region), the rBC particles were strongly compressed in the planetary boundary layer (PBL), and showed a large vertical gradient at the top of the PBL. In contrast, when an air mass originated from the north of BJ (clean region), there was a small vertical gradient. This analysis suggests that there was significant regional transport of rBC particles that enhanced the air pollution in BJ, and the transport not only occurred near the surface but also in the middle levels of the PBL (around 0.5 to 1 km). The measured size distributions show that about 80% of the rBC particles were between the diameters of 70 and 400 nm, and the mean diameter of the peak rBC concentrations was about 180–210 nm. This suggests that the rBC particles were relatively small particles. The mixing state of the rBC particles was analyzed to study the coating processes that occurred on the surface of these particles. The results indicate that the air mass strongly affected the number fraction (NF) of the coated particles. As for a southern air mass, the local air pollution was high, which was coupled with a lower PBL height and higher humidity. Consequently, hygroscopic growth occurred rapidly, producing a high NF value (~65%) of coated rBC particles. The correlation coefficient between the NF and the local relative humidity (RH) was 0.88, suggesting that the rBC particles were quickly converted from hydrophobic to hydrophilic particles. This rapid conversion is very important because it suggests a shorter lifetime of rBC particles under heavily polluted conditions. In contrast, under a northern air mass, there was no clear correlation between the NF and the local humidity. This suggests that the coating process occurred during the regional transport in the upwind region. In this case, the lifetime was longer than the southern air mass condition.