Molybdenum trioxide doped on fibrous silica-titania (MoO3/FST) has been synthesized and evaluated in the catalytic isomerization of C5–C7 for the first time. The structure characterization, functional group, and acid distribution of MoO3/FST were assessed via XRD, N2-physisorption, FTIR, and Py-IR analysis. The IR spectra revealed that MoO3/FST was occupied by a moderate-to-strong Brønsted and Lewis acid sites distribution. By adding MoO3, intense metal-support interactions were formed, lessening Brønsted acid sites' intensity in contrast to the increasing Lewis acid sites' intensity. The isomerization test demonstrated that maximum conversions of 50.0, 80.0, and 84.0% were acquired at 300 °C corresponding to n-C5, n-C6, and n-C7, respectively. As the isomerization temperature rose from 150 to 350 °C, the yield of n-C5 to n-C7 isomers increased to ∼70.0%. The high activity of MoO3/FST was ascribed to the effective interaction between MoO3 with perturbed silanol groups, which led to enrichment in protonic acid site formation via H2 spillover. This finding proves that the isomerization catalysts should possess great Lewis acid and Bronsted acid sites to enrich the protonic acid side, resulting in high performance in isomerization.