Electron ionization-gas chromatography/mass spectrophotometry (EI-GC/MS) is generally used in searching for methcathinone (MCT) analogs. However, the spectrum of EI-GC/MS is difficult to interpret in new psychoactive substances (NPS) that are not registered in GC/MS libraries. There is also a risk of confusion because of the many candidate structures for fragment ions. By using our method, 13 kinds of MCT analogs can be classified into 26 different kinds of fragment ions based on typical and basic fragment ions. In addition, we compared the measured molecular weight (MW) and predicted the structure for the fragment ions of MCT analogs based on the candidates of the structures for their ions by EI-GC/MS and Orbitrap-EI-GC/MS. As a result of the analysis by EI-GC/MS, the MW was measured only up to the first digit. This made it difficult to specify the structure because there are many possible candidates. Whereas in the analysis by Orbitrap-EI-GC/MS, the MW was accurately measured up to the fifth digit. In addition, since the analysis only specified one type of candidate, it could be predicted accurately. Sulfur, iron, chlorine, and bromine, which are compounds with halogen or high isotope ratios, were also clearly distinguished in the analysis by Orbitrap-EI-GC/MS. In conclusion, when unknown NPS evidence is requested, it will be possible to predict the structure more quickly using chemical structural marker-based identification of MCT analogs by Orbitrap-EI-GC/MS. Therefore, this analysis will be useful to prevent the abuse of NPS.