A phenyl-modified silica isoporous membrane (Ph-SIM) was prepared on the indium-tin-oxide (ITO) electrode using the electrochemically assisted self-assembly (EASA) method. The resulting Ph-SIM preserved vertically ordered nanochannels while exhibiting outstanding hydrophobicity due to the incorporation of phenyl groups within the nanochannels. As a result, the Ph-SIM/ITO sensor exhibited a remarkable affinity for PCNB extraction through hydrophobic interactions, leading to high detection sensitivity. The electrochemical response showed a linear enhancement with the logarithmic concentration of PCNB ranging from 0.1 to 20.0µM, and the limit of detection was 4.64nM. Practical results demonstrated that the Ph-SIM/ITO sensor possessed good anti-fouling capability and robust stability, making it a promising candidate for portable detection of non-polar contaminants.