This paper reports the development of fiber optical hydrogen sensors using palladium and gold alloy nanostructures as sensor materials for hydrogen measurements using a D-shaped fiber as a platform. Using a maskless reactive ion etching technique, silica nanocone structures were formed on the surface of the D-shaped fiber. Palladium and gold alloys were deposited on the surface of nanostructured D-shaped fiber to form a nano-alloy sensor film. Evanescent interaction between guided light propagated in the fiber core and nano-alloy enabled highly sensitive hydrogen detection from concentrations that ranged from 0.25% to 10% in atmosphere pressure. The formation of nanostructured alloy enabled by the nanocone surface led to more than 3 times faster in sensor response time and significant improvements in sensor sensitivity and reversibility. The work presented here demonstrates that highly controllable VLSI microfabrication schemes can be applied to produce nanostructured sensor films on optical fibers for high-sensitivity chemical sensing.