A nanocomposite of cobalt nanoparticle (CoNPs) functionalized carbon nanotube (Co@CNT) was prepared to be modified on glassy carbon electrode (Co@CNT/GCE). Characterization indicates the morphology of Co@CNT is CoNPs adhering on CNTs. As the nano-interface, Co@CNT processes large surface area, highly catalytic activity and efficient electron transfer, makes Co@CNT/GCE exhibiting satisfactory electrochemical response toward quercetin (QC) and folic acid (FA). pH investigation indicates the same number of electron and proton involves in the redox process of the analytes, the optimized pH value for the detection of FA and QC is 7.0 and 3.0, respectively. The saturated absorption capacity (Γ*) and catalytic rate constant (kcat) of Co@CNT/GCE for QC and FA are calculated as 1.76×10− 9, 3.94×10− 10 mol∙cm− 2 and 3.04×102, 0.569×102 M− 1∙s− 1. The linear range for both of FA and QC is estimated to be 5.0 nM-10 µM, the LODs (3σ/s) were calculated as 2.30 nM and 2.50 nM, respectively. The contents of FA and QC in real samples determined by Co@CNT/GCE are approximate with the results determined by HPLC. The recoveries were in the range of 90.5%~114% and the total RSD was lower than 8.67%, further confirms the reliability of the proposed electrode for the practical detection.