Digital Annealer developed by Fujitsu is a new architecture to solve “combinatorial optimization problems” at high speed with digital circuit inspired by quantum phenomena. The features are stable operation with digital circuit at room temperature, easy miniaturization, and easy mapping more complex problems with a fully-connected architecture. The Digital Annealer is easy to apply actual problems and contributes to customers in a wide range of businesses, including drug discovery, chemistry, manufacturing, transportation, finance, and logistics. In this article, we explain the fundamental of the Digital Annealer including the speedup technique. We also introduce an application to the material development using the Digital Annealer. The Digital Annealer is used to evaluate the structural similarity of the flavor molecules. We found that the molecules with high structural similarity show a similar flavor. We also extracted the common substructure of molecules having the similar flavor, which is considered to be the key structure of the flavor.