The need for precise modulation of blood concentrations of pharmaceutical molecule, especially for high-risk drugs like Methotrexate (MTX), is underscored by the significant impact of individual variations on treatment efficacy. Achieving selective recognition of pharmaceutical molecules within the complex biological environment is a substantial challenge. To tackle this, we propose a synergistic atomic-molecular docking strategy that utilizes a hybrid-dual single-atom Fe1-Zn1 on a TiO2 photoelectrode to selectively bind to the carboxyl and aminopyrimidine groups of MTX respectively. By integrating this Fe1-Zn1-TiO2 photoelectrode with a microcomputer system, an implantable photoelectrochemical-therapeutic drug monitoring (PEC-TDM) system is developed for real-time, continuous in vivo MTX monitoring. This system facilitates personalized therapeutic decision-making and intelligent drug delivery for individualized cancer therapy, potentially revolutionizing oncological care and enhancing patient outcomes. Concentration of methotrexate (MTX) in the blood needs precise monitoring, Here, the authors propose an atomic-molecular docking strategy that utilizes a hybrid-dual single-atom Fe1-Zn1 on TiO2 photoelectrode to bind to the carboxyl and aminopyrimidine groups of MTX.