Secondary organic aerosol (SOA) exerts a considerable influence on atmospheric chemistry. However, little information about the vertical distribution of SOA in the alpine setting is available, which limited the simulation of SOA using chemical transport models. Here, a total of 15 biogenic and anthropogenic SOA tracers were measured in PM2.5 aerosols at both the summit (1840 m a.s.l.) and foot (480 m a.s.l.) of Mt. Huang during the winter of 2020 to explore their vertical distribution and formation mechanism. Most of the determined chemical species (e.g., BSOA and ASOA tracers, carbonaceous components, major inorganic ions) and gaseous pollutants at the foot of Mt. Huang were 1.7–3.2 times higher concentrations than those at the summit, suggesting the relatively more significant effect of anthropogenic emissions at the ground level. The ISORROPIA-II model showed that aerosol acidity increases as altitude decreases. Air mass trajectories, potential source contribution function (PSCF), and correlation analysis of BSOA tracers with temperature revealed that SOA at the foot of Mt. Huang was mostly derived from the local oxidation of volatile organic compounds (VOCs), while SOA at the summit was mainly influenced by long-distance transport. The robust correlations of BSOA tracers with anthropogenic pollutants (e.g., NH3, NO2, and SO2) (r = 0.54–0.91, p < 0.05) indicated that anthropogenic emissions could promote BSOA productions in the mountainous background atmosphere. Moreover, most of SOA tracers (r = 0.63–0.96, p < 0.01) and carbonaceous species (r = 0.58–0.81, p < 0.01) were correlated well with levoglucosan in all samples, suggesting that biomass burning played an important role in the mountain troposphere. This work demonstrated that daytime SOA at the summit of Mt. Huang was significantly influenced by the valley breeze in winter. Our results provide new insights into the vertical distributions and provenance of SOA in the free troposphere over East China.