Nafion-CaO, Nafion-ZrOH, and Nafion-CaO-ZrOH membranes are fabricated in order to improve proton conductivity, thermal stability, and mechanical properties as well as decrease methanol crossover in direct methanol fuel cells. The ion exchange method is utilized to incorporate Ca and Zr into Nafion membranes. Prepared membranes are characterized by using absorption transmission reflectance (ATR) and energy dispersive X-ray spectroscopy (EDS) techniques. Methanol crossover decreases significantly for all fabricated membranes. Nafion-CaO and Nafion-CaO-ZrOH membranes exhibit a 10 and 6 time increase in proton conductivity compared to Nafion (0.08 Scm–1), while the proton conductivity of Nafion-ZrOH decreases. The elastic modulus enhance from 48 MPa for Nafion to 60, 78, and 90 MPa for Nafion-CaO, Nafion-ZrOH, and Nafion-CaO-ZrOH membranes. In addition, the thermal stability of Nafion (360 °C) increases to 407, 457, and 470 °C for fabricated membranes.