To investigate the molecular characteristics and formation mechanisms of biogenic secondary organic aerosol (BSOA), daytime and nighttime PM2.5 samples were collected at the summit of Mt. Tai during the summer of 2016. The critical indicators of primary sources, such as elemental carbon (EC) and levoglucosan, displayed similar values during the daytime and nighttime, suggesting that changes in the boundary layer heights (BLHs) produced only inconsequential effects during the observation campaign. The molecular distributions of the BSOA were dominated by isoprene SOA tracers (68.5 ± 42.6 ng m–3), followed by monoterpene (43.5 ± 24.4 ng m–3) and β-caryophyllene (16.3 ± 8.6 ng m–3) SOA tracers. Due to the higher diurnal temperatures and solar radiation, the concentrations of all of the tracers were higher during the day than at night. The ratio of the combined cis-pinonic and cis-pinic acid to the MBTCA (P/M) was much lower than in Chinese cities and at the Tibetan background site, indicating that the monoterpene SOA was relatively aged in the mountainous atmosphere, in large part because of the stronger solar radiation at the peak of Mt. Tai. The concentrations of the BSOA products exhibited a significantly positive correlation with the level of ozone during the daytime (R2 = 0.58–0.86) and the temperature over the whole sampling period (R2 = 0.37–0.75), as higher temperatures can accelerate the emission of biogenic volatile organic compounds and the formation of SOA. By contrast, the BSOA tracers displayed a negative linear correlation with the relative humidity (RH) (R2 = 0.43–0.84) and the in situ particle pH (pHis) (R2 = 0.55–0.70) because high RH can inhibit the acid-catalyzed formation of BSOA due to the dilution of the aerosol acidity. No correlation between the BSOA tracers and anthropogenic pollutants (e.g., levoglucosan, SO42–, NO3– and EC) was observed during the daytime or nighttime, suggesting that BSOA tracers in the atmosphere of Mt. Tai during summer were primarily derived from the local oxidation of BVOCs rather than long-distance-transported anthropogenic emissions from the lowlands.