Poly(benzimidazole/ether/siloxane/amide) (PBESA) having siloxane and ether groups in the backbone has been prepared using 4-(3,4-diaminophenoxy)benzene-1,2-diamine, bis(carboxypropy)tetramethyldisiloxane, and 4,4'-oxydianiline via polyphosphoric acid processes with heating up to 160°C. The sulfonation of polystyrene (PS-S) was conducted using 98% sulfuric acid. Afterward, a series of hybrid membranes using PBESA/PS-S/silica nanoparticles (SiNPs) have been developed with 0.1–2 wt% nanofiller. Later, the membranes were doped with phosphoric acid and subjected to various characterization techniques. Field emission scanning electron micrographs (FESEMs) showed gyroid-like patterning of nanoporous membranes with uniform ionic pathways. Fine water retention capability and higher proton conductivity of new hybrids, owing to consistent porous membrane structure, were observed. Increasing the amount of nanoparticles (0.1–2 wt%) also enhanced the tensile stress of acid-doped PBESA/PS-S/SiNPs nanocomposites from 64.9 to 68.1 MPa. There existed a relationship between nanofiller loading and thermal stability of the membranes. The glass transition temperature of phosphoric acid–doped PBESA/PS-S/SiNPs nanocomposites increased from 202 to 214°C. The membranes also had fine ion exchange capacity (IEC) of around 2.5–3.7 mmol g^–1. Novel membranes with high IEC value achieved high proton conductivity of 1.26–2.74 S cm^–1 in a wide range of humidity values at 80°C, which was higher than that for perfluorinated Nafion^® 117 membrane (1.1 x 10^–1 S cm^–1 at 80°C, 94% relative humidity (RH)). The fuel cell (hydrogen/oxygen) using PBESA/PS-S/SiNPs 2 (IEC 3.7 mmol g^–1) showed better performance than that of Nafion^® 117 at 40°C (30% RH).