Aluminosilicate zeolite YNU-5, whose framework type code is YFI , has a unique pore structure consisting of 12–12–8-ring three-dimensional pores and isolated 8-ring straight channels. In this study, we evaluated how the crystal structure of zeolite YNU-5 changed by ammonium ion exchange and acid treatment by structural analysis using powder X-ray diffraction and solid-state MAS NMR spectroscopy. While the elemental ratio of calcined YNU-5 is Si/Al = 9.0, K/Al < 0.52, and Na/Al < 0.12, those of ammonium ion-exchanged sample were Si/Al = 9.3, K/Al < 0.03, and Na/Al < 0.03. That is, most alkali metal cation was exchanged to ammonium ion while suppressing dealumination. In an acid-treated sample with 2 M nitric acid at 353 K for 2 h under stirring conditions (milder dealumination conditions), dealumination took place and Si/Al was increased to 39.4, and almost all alkali metal ions were removed (K/Al < 0.3, and Na/Al < 0.2). When treated with 13.4 M nitric acid for 24 h under reflux conditions (severer dealumination conditions), deep dealumination occurred (Si/Al ~ 300) and the alkali metal ions were hardly detected. The structure refinement by the Rietveld method strongly suggested the presence of Si atom vacancies due to dealumination in the sample after milder acid-treatment conditions. In contrast, Si atom vacancies at specific T sites in the sample after severer acid-treatment conditions were hardly detected even though the presence of a small amount of Q 3 Si atom species ((SiO) 3 Si –OH) with silanol group was identified by 29 Si MAS NMR measurement. This finding suggests that almost all Al atoms were replaced by Si atoms migrated in nanopores and the vacancies are distributed uniformly at every T sites. By reflux acid treatment, the zeolite YNU-5 changed from the aluminosilicate type to the high silica type while maintaining high structural stability and high crystallinity. • Crystal structures of ammonium ion-exchanged and two kinds of dealuminated zeolite YNU-5 were analyzed in detail. • Simultaneously with dealumination, the Si atom migration phenomenon occurs during acid treatment. • The structural thermal stability of zeolite YNU-5 is strongly related to the distribution of T-atom vacancies in the framework.