Carbon (C), nitrogen (N) and phosphorus (P) concentrations and stoichiometry play important roles in biogeochemical cycles of the ecosystems, yet it is still unclear how the allocations of C, N and P concentrations and stoichiometry among plant organs and soils related to O3 stress and straw return. Here, a pot experiment was conducted in open top chambers to monitor the response of C, N and P concentrations and stoichiometry of leaves, stems, roots and soils during a growing season (branching, flowering and podding stages) of soybean (Glycine max; a species highly sensitive to O3) to background O3 concentration (44.8 ± 5.6 ppb), O3 stress (79.7 ± 5.4 ppb) and straw treatment (no straw return and straw return). O3 stress significantly decreased root biomass. Straw return significantly increased root biomass under O3 stress at branching and flowering stages. Generally, O3 stress and straw return showed significant effects on the C, N and P concentrations of leaves and soils, and stoichiometric ratios of leaves, stems and microbial biomass. The C, N and P concentrations and stoichiometry of leaves, stems, roots and soils in response to O3 stress and straw return at the branching stage were inconsistent with the changes observed at the flowering and podding stages. The P conversion efficiency showed significant relationship with root P concentration under the combined effects of O3 stress and straw return. Altogether, the present study indicated that C, N and P concentrations of soybean might be more important than stoichiometric ratios as a driver of root defence against O3 stress in the case of straw return.