Against the theoretical limitations and practical challenges of directly adopting tax rates specified in the Environmental Protection Tax Law of People’s Republic of China as substitution costs, this study establishes a multi-method framework for apportioning the operating costs of wastewater treatment, aiming to calculate pollutant removal unit costs that more closely reflect actual abatement costs. Using nationwide macro-statistical data of centralized wastewater treatment plants from 2015 to 2023, the unit operating costs for removing COD Cr, TN and TP are quantified via four approaches:characterization factor method, comprehensive trophic state index method, equivalent pollution load method, and environmental protection tax (EPT) pollution equivalent method. The results indicate that, compared with the cost allocation derived from EPT pollution equivalent method, all alternative methods reveal that the prevailing EPT criteria substantially underestimate the purification value of TN and TP. Optimized based on the equivalent pollution load method (using non lake/reservoir limit values for TP), the cost apportionment ratios for COD Cr, TN and TP are set at 25%, 55% and 20%, respectively. Accordingly, the 2023 unit prices for wetland purification service are calculated as 3.3 CNY/kg for COD Cr, 59.3 CNY/kg for TN and 167.3 CNY/kg for TP. Developed on basis of actual operating expenditure of domestic wastewater treatment facilities, the proposed pricing system overcomes current limitations of using environmental protection tax rates in ecosystem service valuation and provides robust scientific support for gross ecosystem product (GEP) accounting, eco compensation standard setting and EPT environmental reform.