The development of a universal approach for precisely tuning the electrochemical characteristics of conducting carbon nanotubes for tracking harmful agents in the human body with high selectivity and sensitivity remains a challenge. Herein, we describe a simplistic, versatile, and general approach to the construction of functionalized electrochemical material. The design of electrochemical material consists of (i) modification of multiwalled carbon nanotubes (MWCNT) with dipodal naphthyl‐based dipodal urea (KR‐1) through non‐covalent functionalization (KR‐1@MWCNT) which enhances the dispersibility of MWCNT and hence conductivity, (ii) complexation of KR‐1@MWCNT with Hg2+ accelerate the electron transfer in the material which amplify the detection response of functionalized material (i. e., Hg/KR‐1@MWCNT) towards various thymidine analogues. Further, the application of functionalized electrochemical material (Hg/KR‐1@MWCNT) achieves real‐time electrochemical monitoring of harmful antiviral drug 5‐iodo‐2’‐iododeoxyuridine (IUdR) levels in human serum for the first time.