Due to low working temperature, high energy density and low pollution, proton exchange fuel cells have been investigated under different operating conditions in different applications. Using platinum catalyst in methanol fuel cell leads to increasing the cost of this kind of fuel cells which is considered as a barrier to commercialism of this technology. For this reason, a lot of efforts have been made to reduce the loading of the catalyst required on different supports. In this study, carbon black (CB) and carbon nanotubes (CNT) have been used as catalyst supports of the fuel cell as well as using the double-metal combination of platinum-ruthenium (PtRu) as anode electrode catalyst and platinum (Pt) as cathode electrode catalyst. The performance of these two types of the electro-catalyst in oxidation reaction of methanol has been compared based on electrochemical tests. Results showed that the carbon nanotubes increase the performance of the micro-fuel cell by 37% at maximum power density, compared to the carbon black. Based on thee-electrode tests of chronoamperometry and voltammetry, it was found that oxidation onset potential of methanol for CNT has been around 20% less than CB, leading to the kinetic improvement of the oxidation reaction. In addition, the active electrochemical surface area of catalyst has been increased up to 90% by using CNT compared to CB which shows the significant rise of the electrocatalytic activity in CNT supported catalyst with 62% increase in current density of methanol oxidation reaction respect to CB supported one. Moreover, the resistance of CNT supported sample to poisonous intermediate species has been found 3% more than CB supported one. According to the chronoamperometry test results, it was concluded that the performance and sustainability of NCT electro-catalyst shows remarkable improvement compared to CB electro-catalyst in long term.