Chemical inhibitors are essential for controlling polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs) formation during municipal solid waste incineration, while conventional N-S-based inhibitors emit secondary pollutants such as NOx and SO2. Developing novel inhibitors is crucial to reduce secondary pollution. Here, the N-P-based inhibitors diammonium hydrogen phosphate (DAP) and ammonium polyphosphate (APP) were proposed to explore the inhibition effects and mechanisms of PCDD/Fs. The findings demonstrated that using DAP at a 1% mass ratio in the model fly ash (MFA) significantly increased I-TEQ inhibition efficiency to 98.8%, a 27.4% improvement compared to the standard inhibitor, thiourea (TUA). The inhibition mechanisms were investigated through experiments and density functional theory (DFT) calculations. We observed that the phase transition (from CuCl2 to CuHPO4, Cu2P2O7) weakened the catalytic action of CuCl2, while the chlorination action of CuCl2 was also blocked during PCDD/F formation. TGA-MS results showed DAP and APP released NH3, which consumed Cl2 and impeded the chlorination process. Furthermore, they were more eco-friendly than TUA, as they did not emit NOx or SO2. Additionally, DFT calculations revealed that inhibitors impaired the catalysis process, ranked by binding energy to the catalyst: Ebenzene-b (−0.59 eV) > EHPO4-b (−3.15 eV) > ENH4-b (−3.24 eV) > EP2O7-b (−4.67 eV) > ECH4N2S-b (−11.38 eV). Moreover, economic feasibility analysis indicated that the DAP and APP had large cost advantages over the TUA, reducing costs by 67.7% and 19.8%, respectively. The proposed strategy, which achieved superior inhibition effects for PCDD/Fs and reduction of inhibitor costs, appears promising for industrial application.