Eucalypts are important forest resources in southwestern China, and may be tolerant to elevated ground-level ozone (O3) concentrations that can negatively affect plant growth. High CO2 may offset O3-induced effects by providing excess carbon to produce secondary metabolites or by inducing stomatal closure. Here, the effects of elevated CO2 and O3 on leaf secondary metabolites and other defense chemicals were studied by exposing seedlings of Eucalyptus globulus, E. grandis, and E. camaldulensis × E. deglupta to a factorial combination of two levels of O3 (< 10 nmol mol−1 and 60 nmol mol−1) and CO2 (ambient: 370 μmol mol−1 and 600 μmol mol−1) in open-top field chambers. GC-profiles of leaf extracts illustrated the effect of elevated O3 and the countering effect of high CO2 on compounds in leaf epicuticular wax and essential oils, i.e., n-icosane, geranyl acetate and elixene, compounds known as a first-line defense against insect herbivores. n-Icosane may be involved in tolerance mechanisms of E. grandis and the hybrid, while geranyl acetate and elixene in the tolerance of E. globulus. Elevated O3 and CO2, singly or in combination, affected only leaf physiology but not biomass of various organs. Elevated CO2 impacted several leaf traits, including stomatal conductance, leaf mass per area, carbon, lignin, n-icosane, geranyl acetate and elixene. Limited effects of elevated O3 on leaf physiology (nitrogen, n-icosane, geranyl acetate, elixene) were commonly offset by elevated CO2. We conclude that E. globulus, E. grandis and the hybrid were tolerant to these O3 and CO2 treatments, and n-icosane, geranyl acetate and elixene may be major players in tolerance mechanisms of the tested species.