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Polyethylene (PE) plastics are extensively utilized across agricultural, industrial, and medical sectors owing to their favorable physicochemical properties. However, their chemical stability and escalating production have resulted in severe waste accumulation and environmental pollution. Conventional disposal methods are plagued by resource inefficiency and secondary pollution. While emerging strategies offer promise, physicochemical methods demand harsh operating conditions, and biological routes remain inefficient. This research presents an integrated “chemical pretreatment–biodegradation–upcycling” system that combines the efficiency of chemical catalysis with the sustainability of biological conversion. Ester bonds were introduced into PE via Baeyer–Villiger oxidation, followed by enzymatic hydrolysis using the cutinase from Thermobifida fusca WSH03-11 ( Tf Cut). Specifically, machine learning-aided optimization of reaction conditions and computational redesign of Tf Cut enhanced degradation efficiency, yielding a maximum weight loss of approximately 71.19%. The degradation intermediates were bio-converted into poly(3-hydroxybutyrate) (PHB) by the wild-type strain LETBE-HOU, isolated in this study, achieving a concentration of 16.75 mg/L. Multi-omics analysis of LETBE-HOU further revealed the PHB biosynthesis pathway and fatty acid degradation regulation. This work breaks the long-standing reliance on physiochemically-derived degradation intermediates for microbial conversion of PE, establishing a fully circular system that opens new avenues for future research.