Thiamethoxam is one of the main suspect in honeybee colony collapse disorder (CCD). Due to this reason, thiamethoxam including imidacloprid and clothianidin has been banned for two years in some Europe countries. The CCD phenomenon has also been reported in Korea. Regarding this issue and needs, a new project has started to develop the method for the quatitation of thiamethoxam using isotope dilution mass spectrometry (IDMS). In the process of optimization for the IDMS method with thiamethoxam and thiamethoxam-d3, we observed that the fragment peaks did not correspond to the fragmentation pathway as published elsewhere. Here, we proposed a candidate fragmentation pathway. To validate the proposed fragmentation pathway, another isotope analogue, thiamethoxam-d4, was introduced and the MS/MS spectra of both isotope analogues were compared. In addition, the MS/MS/MS spectra of thiamethoxam were inspected for more evidence of the candidate pathway. Those spectra indicated that the proposed fragmentation pathway could be used to assign the fragment peaks of thiamethoxam.