Green stem disorder (GSD) in soybean (Glycine max (L.) Merrill) negatively affects harvest efficiency and seed appearances. Breeding GSD-insensitive cultivars is expected to be an effective countermeasure to GSD. However, it is difficult to stably detect cultivar differences in GSD under conventional field conditions because the occurrences of GSD largely vary by location and year. The thinning effect, which had been reported to promote GSD, may help accurate phenotyping for occurrences of GSD in breeding. To verify this possibility, the thinning treatment was applied to four cultivars, the GSD severity values of which were evaluated in an independent study by another group. As a result, the cultivar differences in GSD severity were generally comparable between the present and previous studies. However, the difference was more evident, with the thinning treatment exhibiting the GSD score of 2.8 of 'Hatsusayaka' compared with the GSD score of 3.6 of 'Sachiyutaka', while the scores of those cultivars were similar without the thinning treatment. A positive correlation between GSD severity and N concentration in the main stem could be seen but the increasing rate of GSD score with the N concentration in the main stem differed between cultivars. Thus, although more cultivars need to be tested to prove, the thinning treatment could be useful as a phenotyping technique in the breeding of GSD-insensitive cultivars.