The development of high conductivity proton exchange membranes (PEM) with efficient ion channels is a focus of fuel cell research. In this work, PEMs based on sulfonated polyimide are prepared by a simple synthesis route. The conformational change of the polymer depends on the type of polymeric chemical structure, leading to the formation of nanoscale cavities and ion channels for rapid proton transport, as evidenced by micropore porosities tests and proton conductivity tests. CO2 adsorption and desorption curves determined that the pore distribution of the polymer is 0.3–1.5 nm, and the specific surface area is up to 106.644 m3g−1, and the microphase separation channels are measured by X-ray diffraction. The introduction of microporous structures and microphase separation channels work together to make excellent electrochemical performance. The proton conductivity of SPI-B40 with the ion-exchange capacity (IEC) of 1.76 mmol g−1 is up to 0.146 S cm−1 at 80 °C, and the power density can reach 869 mW cm−2.