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The incorporation of straw with a microbial inoculant (a mixture of bacteria and fungi, designed to accelerate straw decomposition) is being increasingly adopted within the agricultural sector in China. However, its effects on N and C trace gas emissions remain unclear. We conducted a field experiment to investigate the effects of different straw incorporation methods (with and without microbial inoculant) in the wheat season on nitrous oxide (N2O) and methane (CH4) emissions from a wheat-rice rotation system in China. The treatments comprised N, P, and K fertilizers only (NPK), NPK plus rice straw (NPKS), NPKS plus Ruilaite microbial inoculant (NPKSR), and NPKS plus Jinkuizi microbial inoculant (NPKSJ). Rice straw incorporation before wheat sowing significantly decreased N2O emissions during the wheat season and stimulated N2O and CH4 emissions during the subsequent rice season. Compared with the NPKS treatment, the NPKSR and NPKSJ treatments decreased N2O emissions during the wheat season, but had no effect on N2O or CH4 emissions during the subsequent rice season. Annually, the two treatments were comparable regarding N2O emissions.Although the global warming potentials of the NPKSR and NPKSJ treatments were lower than that of the NPKS treatment during the wheat season, no significant differences were observed during the subsequent rice season, or over the entire rotation cycle. The annual greenhouse gas intensity was slightly lower in the NPKSR and NPKSJ treatments than in the NPKS treatment. Overall, these results suggest that the incorporation of rice straw with a microbial inoculant in the wheat season was the best strategy tested for managing straw resources within the wheat-rice rotation system.