Temperature-dependent structural investigations of layered pentaborate NaSr[B5O9] belonging to a family of compounds with the general formula A+B2+[B5O9] (A = Na, K; B = Ca, Sr, Ba, Pb) have been performed. The thermal expansion shows slightly anisotropic behavior (α11 = 7, α22 = 10, α33 = 22 × 10-6 °C1- at 100 °C) which is caused by preferential orientation of the pentaborate [B5O11] rigid groups (fundamental building units, FBUs) of the layer. The monoclinic β angle increases above 600 °C due to a heterovalent Sr2+ ↔ Na+ cation substitution. Members of the A+B2+[B5O9] family are represented by two structural types which are characterized by the different orientations of the pentaborate FBUs within the layers. A topological analysis of the layers has been made, and corresponding classifications of the cationic net are given. It was found that the type of the structure strongly depends on the difference in the ionic radii of alkaline A+ and alkaline-earth B2+ cations. Our ab initio calculations also indicate the KCa[B5O9] compound unstability. Based on the density functional theory (DFT) calculations, it was also shown that the compound KCa[B5O9] is unstable under ambient conditions. According to the geometry analysis, the reason for the instability is the K+ and Ca2+ cations are size mismatched.