Nb-Ti-Ni alloy is one of the candidates for hydrogen permeation membranes. The hydrogen permeability of a membrane depends on its thickness, and mechanical properties such as the fracture toughness of the membrane are important to ensure reliability and durability. In the present work, micro-mechanical tests have been carried out for melt-spun Nb-Ti-Ni thin films consisting of amorphous and nano-crystalline phases. The relationship between the mechanical properties of the melt-spun films and the microstructural changes occurring in the films due to heat treatment has been also discussed. The Nb-Ti-Ni alloy thin films were prepared by the melt-spun technique and then heat-treated at 873-1173 K. Micro-sized cantilever specimens with dimensions of 10 × 10 × 50 μm3 were prepared by focused ion beam (FIB) machining. Fracture tests were carried out using a mechanical testing machine for the micro-sized specimens; the testing machine was developed by us. In addition, microstructures were observed by transmission electron microscopy (TEM). The fracture toughness (KQ) value decreased up to 823 K, and it increased above 1173 K. The specimen heat-treated above 1173 K showed ductile fracture. The fracture morphology of the specimen heat-treated up to 1023 K showed grain boundary fracture characteristics, and that of the specimen heat-treated at 1173 K changed to transgranular fracture.