Developing proton-exchange membranes (PEMs) for energy applications is necessary for fulfilling the increasing energy demand without environmental effects. In this study, we prepared composite membranes containing mercaptoethanol-assisted sulfonic acid-functionalized polysiloxanes (MASFPs) and perfluorinated sulfonic acid (PFSA). The MASFP-containing composite membrane (i.e., CMASFP-2) exhibited better membrane properties than the composite membrane prepared without mercaptoethanol (CMASFP-1) and the reference Nafion 212 membrane. Wide-angle X-ray diffraction (XRD) studies revealed a broad peak at 2θ = 17.4° and 39°, indicating that the composite membranes are semicrystalline. Scanning electron microscopy (SEM) analysis revealed that the prepared composite membranes had good morphology, whereas energy-dispersive X-ray spectroscopy analysis revealed that it had siloxane and more sulfonic acid than the pristine PFSA membrane. Thermogravimetric and mechanical strength analyses revealed that incorporating sulfonic acid-functionalized siloxanes improved the thermal stability and mechanical strain of the membrane. The prepared CMASFP-2 membrane had a high ionic conductivity of 0.106 mS cm−1 and an ion-exchange capacity of 1.09 meq·g−1. CMASFP-2 also exhibited lower hydrogen gas permeability than the Nafion 212 and PFSA membranes, demonstrating that it can be used for energy applications.