The present invention provides a method for evaluating a synthetic aptitude of a compound, a program for evaluating a synthetic aptitude of a compound, and a device for evaluating a synthetic aptitude of a compound, which evaluate a synthetic aptitude of a compound generated and/or modified on a computer. The present invention relates to a method for evaluating a synthetic aptitude of a compound, the method including a step of selecting a compound database storing a plurality of reference compounds, a step of deciding a structure of a compound to be evaluated for the synthetic aptitude, a step of extracting a reference atomic arrangement from a structure of the reference compound stored in the compound database and obtaining a reference appearance frequency of the reference atomic arrangement, a step of extracting an atomic arrangement from the structure of the compound and obtaining an appearance frequency of the atomic arrangement, and a step of evaluating the synthetic aptitude based on the number of bonds included in the atomic arrangement of the compound and the appearance frequency of the reference atomic arrangement corresponding to the atomic arrangement; a program to execute the method; and a device to execute the method.