The authors have investigated the structure and the composition of the barrier in YBCO vertically-stacked-type interface-treated Josephson junctions by TEM and TEM-EDS. The barrier was formed by the Ar ion milling of the base YBCO electrode surface and the subsequent annealing. For a sample treated with accelerating voltage ( acc ) of 1300 V, we observed Y 2 O 3 phases in the barrier. In contrast, for a sample with acc = 700 V, we could observe few Y 2 O 3 phases. Our TEM observation suggested that junctions with higher c fabricated with lower acc would have thinner and more uniform barriers. In addition, the composition of the barrier was Y-rich and Cu-poor, and such deviation decreased with decreasing acc . These tendencies well correspond to the results for ramp-edge-type junctions reported so far.