Numerous interrelated factors (e.g., the labile C, soil NO3− concentration, and soil moisture content) are involved in controlling the microbial sources of N2O and the product stoichiometry of denitrification; however, the interactions among different factors are still poorly understood. Here, a fully robotized continuous flow soil incubation system (allowing simultaneous measurements of N2 and N2O fluxes) was employed to investigate the interactive effects of a 51-day duration of moist spell, straw amendment, and the NO3− level on the rate and product stoichiometry (N2O/(N2O + N2) ratio) of denitrification in heavily N loaded arable soils (i.e., paddy, vegetable, and orchard soils). The rewetting-induced N2O emissions mainly originated from bacterial denitrification in all soil types, with a clear shift to fungal denitrification (plus contingent nitrification) over time. The vegetable and orchard soils showed a higher share of bacterial N2O (62–70%) than that in the paddy soils (50–54%), which may be attributed to more labile-C driven bacterial activity induced by the greater manure and crop residue input therein. Interestingly, the inhibitory effect of high soil NO3− on N2O reduction in these soils was offset by a 51-day-long moist spell, regardless of the amendment of straw. To our knowledge, our study is the first to show that the inhibitory effect of high residual NO3− on N2O reduction is suppressed by a moist spell with a certain duration in heavily N loaded arable soils, suggesting that the water regime history should be considered when optimizing the N fertilizer application timing to mitigate soil N2O emissions.