To explore the responses of different pH soils to Cu and Zn residues in the swine manure from intensive animal husbandry, three vegetable-planted soils with the acidic (pH 5.81), neutral (pH 7.18) and alkaline (pH 8.00) were used to treat with an addition of zero manure (CK), organic manure (M) and polluted manure (MP), respectively. All treatments were incubated for half year under the alternation of dry and wet conditions to exhaust the available carbon and nitrogen from the manure. After that, urea was added to each treatment to examine effects of residual Cu and Zn on N2O emissions and its related factors. The results show that N2O emissions from different pH soils had different responses to MP addition. MP significantly reduced N2O emissions from acidic and alkaline soils, while significantly increased N2O emissions from neutral soil (P2O-producing substrates and microbial factors significantly related to available Cu and Zn in different soils. Further stepwise regression analysis showed that the main drivers of N2O emissions from acidic soil were NH4+-N conversion amount, available Zn content and 18S rRNA abundance. N2O emissions from alkaline soil were decided by NO3--N production level only, while the main driver of N2O emissions from neutral soil was the available Cu content. Relative to M treatment, residual available Cu in MP was significantly negatively correlated to the nirS abundance (P0.95); the residual Cu had the greatest role in acidic soil compared to other soils. The residual Zn was positively correlated with nosZ(P0.95), and had the largest promoting effect in neutral soil. Evidently, the effective Cu and Zn residues in MP have an overall inhibitory effect on N2O emission-related microbial genes in alkaline soil. Therefore, alkaline soil should be given priority to reduce the negative environmental and ecological effects of manure in intensive aquaculture if the manure is required to return to the field. © 2023 Chinese Society for Environmental Sciences. All rights reserved.