The chemical industry has witnessed a heavy global environmental clean-up and remediation burden. Chemical industrial parks (CIPs) are important carriers of the chemical industry and present both opportunities and challenges in terms of environmental sustainability. The end-of-pipe waste treatment system, comprised of enterprise facilities and shareable infrastructure, is mandatory in Chinese CIPs; in that sense, its cost is often taken for granted without accurate calculation, and reduction opportunities are commonly missed. Quantifying the whole-process cost is thus crucial for promoting the waste treatment system of CIPs. This study established a bottom-up and trilayer nested model for waste treatment, which integrated interphase material flows, pollutant reduction technology, and whole-process cost accounting by targeting CIPs. The cost included wastewater treatment, waste gas treatment, and solid waste disposal costs, and each component further included depreciation, operation, and other expenditures. After empirically applying the model to a typical CIP in China, we revealed that this CIP attained a total waste treatment cost of 1.31 billion CNY (0.19 billion US dollars) in 2016, which is approximately 52.4% of the park's tax income. Overall, approximately 55.6% of the cost was attributable to wastewater treatment (729 million CNY, 108 million US dollars), 12.5% to waste gas treatment, and 31.9% to solid waste disposal. In the empirical case study, the cost imposed a substantial economic burden on the industrial park, while the environmental performance of the waste treatment system still required improvement. The results called for systematic rethinking which is featured by an extended system boundary and three dialectical relations in CIPs. Three policy recommendations were proposed by systematic rethinking, including symbiotic solutions targeting waste treatment infrastructures within and among enterprises, priority optimization on the key enterprises with high pollution emissionsand treatment costs, and flexible deployment of in-plant waste treatment facilities.