Organic peroxides play a vital role in the formation, evolution, and health impacts of atmospheric aerosols, yet their molecular composition and fate in the particle phase remain poorly understood. Here, we identified, using iodometry-assisted liquid chromatography mass spectrometry, a large suite of isomer-resolved peroxide monomers (C8–10H12–18O5–8) and dimers (C15–20H22–34O5–14) in secondary organic aerosol formed from ozonolysis of the most abundant monoterpene (α-pinene). Combining aerosol isothermal evaporation experiments and multilayer kinetic modeling, bulk peroxides were found to undergo rapid particle-phase chemical transformation with an average lifetime of several hours under humid conditions, while the individual peroxides decompose on timescales of half an hour to a few days. Meanwhile, the majority of isomeric peroxides exhibit distinct particle-phase behaviors, highlighting the importance of the characterization of isomer-resolved peroxide reactivity. Furthermore, the reactivity of most peroxides increases with aerosol water content faster in a low relative humidity (RH) range than in a high RH range. Such non-uniform water effects imply a more important role of water as a plasticizer than as a reactant in influencing the peroxide reactivity. The high particle-phase reactivity of organic peroxides and its striking dependence on RH should be considered in atmospheric modeling of their fate and impacts on aerosol chemistry and health effects.