Estradiol (E2), a typical endocrine disruptor, threatens ecological health, while traditional biochar faces limitations in adsorption efficiency and microbial regulatory mechanisms. This study systematically analyzed the effects of twice ball-milled magnetic biochar (TmMBC) on the degradation kinetics, metabolic networks, and microbial-driven mechanisms of E2. The results indicated that TmMBC possesses a specific surface area of 259.59 m2/g and a micropore volume of 0.10 cm3/g. The significantly enhanced active sites (Fe-O, C=O) improve adsorption performance, reducing the half-life of E2 to 1.73 days (compared to 2.11 days in the single application group) and facilitating the conversion of intermediate products estrone and estriol. Compared to single E2 application, TmMBC co-treatment reduced levels by 9.57 % on day 1, which significantly increased above the single group by day 10 (P < 0.05). Metabolomics analysis revealed 513 differential metabolites (312 upregulated) shared between the mixed and single application E2 treatments, which were enriched in carbon fixation and TCA cycle pathways. The abundance of actinobacteria was found to be 17.35 % higher than in the single application group (P < 0.05), and the expression of ABC transporter genes was enhanced. Structural equation modeling indicated that TmMBC drived the accumulation of metabolites (path coefficient = 0.81∗∗) by improving soil physicochemical properties (R2 = 0.999), thereby inhibiting E2 residues. The conclusions suggest that TmMBC efficiently removes E2 through physicochemical metabolism and multidimensional microbial interactions, alleviating oxidative stress toxicity, thereby establishing a foundation for designing composite biochar and advancing soil remediation technologies while offering theoretical and technical support for farmland estrogen pollution management.