In the membrane forming process of a proton exchange membrane fuel cell (PEMFC), drying and annealing heat treatment processes are required for performance and durability. In this study, the optimal annealing temperature for improving the durability of the polymer membrane was studied. It was annealed in the temperature range of 125~175 °C, and thermal stability and hydrogen permeability were measured as basic data of durability at each annealing temperature. The electrochemical durability was analyzed by Fenton reaction and open circuit voltage (OCV) holding. The annealing temperature of 165 °C was the optimal temperature in terms of thermal stability and hydrogen permeability. In the Fenton reaction, the fluorine emission rate of the membrane annealed at 165 °C was the lowest, and the lifespan of the membrane annealed at 165 °C was the longest in the OCV holding experiment, confirming that 165 °C was the optimal temperature for the durability of the polymer membrane.