Optical fiber hydrogen sensing with high sensitivity and fast response is the future developmental direction in hydrogen sensing technology that will be of great importance in ensuring the safety of hydrogen energy systems. To solve the difficulty in coupling palladium-based hydrogen sensitive materials at the nanoscale to optical devices, Au-Pd core-shell nanoparticle films with rapid hydrogen response characteristics were prepared by aqueous phase synthesis and centrifugal deposition. With an array of Au-Pd core-shell nanoparticle films, a transmission sensing system was established in which optical signals could be coupled with the multilayer nanoparticle membrane array. Consequently, the sensitivity of the sensing system was enhanced by improving the modulation capacity of sensing materials to the optical signal. The experimental results show that the Au-Pd core-shell nanoparticle membrane prepared in this study has a particle size of 48 nm and a Pd layer thickness of 4 nm. The response time of the sensitive film to 4% hydrogen concentration is less than 3 s and exhibited good repeatability and stability in the cyclic test. The sensors sensitivity is increased to a factor of 2.7 higher than that of the single film without affecting its response speed. This research can provide important guidance for the development of high-performance optical fiber hydrogen sensors.