In this research, indium ions were introduced into polyoxoniobates (PONbs) reaction systems to facilitate the construction of different {SiNb18O54}-based aggregates, including an {In(en)2{SiNb18O54}2} (en = ethylenediamine) dimer, an {[InO2][In2(en)O3]2{SiNb18O54}3} trimer, and an {[In(en)2][InO2][In7(en)5O9]{SiNb18O54}4} tetramer. Interestingly, these aggregates were further assembled into three uncommon extended PONb architectures in the presence of [Cu(en)2]2+ complexes, namely, H3[Cu(en)2(H2O)][Cu(en)2]6[Cu(en)2]2{[In(en)2][K2{SiNb18O54}(H2O)6]2}·1.5en·16H2O, H9{[Cu(en)2]6{[Cu(en)2]3[Cu(en)2(H2O)][In(H2O)2][In2(en)(H2O)2(OH)]2{SiNb18O54}3}·5en·29H2O, and H14[Cu(en)2]0.5[Cu(en)2(H2O)]{[Cu(en)2]2{[Cu(en)2]3[Cu(en)2(H2O)]5[K(H2O)2][In(H2O)2][In(en)2][In7(OH)9(en)5]{SiNb18O54}4}·7en·39H2O. In addition, all of them have good water vapor adsorption capacities and moderate proton transport capabilities. The above results indicate that introducing suitable heteroatoms to induce the aggregation PONb building blocks and further assembling them into new structures is an effective strategy to enrich the PONbs' structural diversity and develop new functional materials.