An increasing trend in aerosol concentration has been observed in Himalayas in recent years, but the understanding of the chemical composition and sources of aerosol remains poor. In this study, molecular chemical composition of water soluble organic matter (WSOM) from two filter samples (denoted as F30 and F43) collected during high aerosol loading periods at a high altitude station (Qomolangma Station, QOMS, 4276 m a.s.l.) in the northern Himalayas were identified by positive electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI-FTICR-MS). More than 4500 molecular formulas were identified in each filter sample which were classified into two compound groups (CHO and CHON) based on their elemental composition with both accounting for nearly equal contributions in number (45 %–55 %). The relative abundance weighted mole ratio of O / C w for F30 and F43 are 0.43 and 0.38, respectively, and the weighted double bond equivalent (DBE w ), an index for the saturation of organic molecules, were 6.26 and 6.92, respectively, suggesting their medium oxidation and saturation degrees. Although the O / C w mole ratio was comparable for CHO and CHON compounds, the DBEw was significant higher in CHON compounds than CHO compounds. More than 50 % molecular formulas in Van Krevelen (VK) diagram (H / C vs. O / C) located in 1–1.5 (H / C) and 0.2–0.6 (O / C) regions, suggesting potential lignin-like compounds. The distributions of CHO and CHON compounds in VK diagram, DBE vs. number of C atoms, and other diagnose diagrams showed highly similarities between each other suggesting their similar source and/or atmospheric processes. Detailed molecular information in the common formula of these two filters was explored. Many formulas with their homologous series of compounds formed from biogenic volatile organic compounds and biomass mass burning emitted compounds were found in the WSOM with high relative abundance suggesting the important contribution of these two sources in Himalayas. The high DBE and high nitrogen containing of aerosol would have important implication for aerosol light absorption and biogeochemical cycle in this remote region.