NH₃-plasma treated multi-walled carbon nanotubes (pn-MWCNTs) were prepared based on the plasma technique and developed as sensing materials for detection of quercetin and kaempferol with the differential pulse voltammetry (DPV) and amperometric measurement. Such experimental parameters as pH values, accumulation potential and accumulation time were carefully investigated. The pn-MWCNTs modified electrode (pn-MWCNTs/GCE) was further explored for the analysis of quercetin and kaempferol in diluted blood serum and average recovery rates of 96.91 and 100.5% were obtained, respectively. In addition, the interference and stability measurements were evaluated under the optimized experimental conditions. More importantly, selective detection toward quercetin and kaempferol was achieved, and the proposed electrochemical sensing strategy was available to distinguish substances with similar oxidation potential.