Nanostructured MoO3 films were deposited on glass by an atmospheric solid-fed flame vapor deposition (SF-FVD) technique at different substrate temperatures (25 (SRT), 300 (S300) and 400 °C (S400)). FESEM showed web-like morphology for SRT and S300 and plate-like for S400. TEM revealed existing spherical at lower and 2D structures at higher temperatures. Monoclinic and orthorhombic phases were observed for SRT and S300/S400, respectively. With a sputter-deposited Pd film, MoO3 films turn dark blue after hydrogen exposure, for which localized surface plasmon resonance (LSPR) absorption bands have appeared in the NIR region. The LSPR showed a linear blue shift up to 35 nm with < 4% hydrogen concentration. Using a 640 nm LED light source, the capability at very low concentrations of hydrogen and different working temperatures (up to 200 °C) was investigated. Significant sensitivity was observed with a sigmoidal behavior toward hydrogen concentration (0.05–10%). Also, the repeatability and selectivity among interfering gases were desirable. Sample S300 at a working temperature of 150 °C showed the best sensing performance in coloration, reversibility and response time. Raman, XRD and FESEM were used that reveal structural and morphological degradation, where the partial formation of molybdenum oxide bronze (H0.93MoO3) was observed.