This Article presents the systematic experimental and theoretical investigation of the structural arrangements of dodecyl sulfate (DS) anions in the interlayer space of layered zinc hydroxide salts (LZH-DS) and of the structure of zinc hydroxide layers, with a detailed description of the zinc ions’ coordination environment. As-prepared, well-crystalline LZH-DS has a basal spacing of 31.5 Å. After treatment with methanol at room temperature, zinc hydroxide layers shrank to form two new layered phases with basal spacings of 26.4 and 24.7 Å. The shrinking was accompanied by a decrease in the content of DS anions in the interlayer space, indicating a change in the alignment of the intercalated anions and a decrease in the charge density of the zinc hydroxide layers. The latter effect was assessed by the atomic pair distribution function (PDF) analysis of powder X-ray diffraction patterns, revealing the successive removal of Zn ion tetrahedra from the hydroxide layers, with the octahedrally coordinated Zn ions left unaffected. The interlayer space of all three phases was modeled by molecular dynamics, and the models were validated by the comparison of modeled and experimental powder XRD patterns and one-dimensional electron density maps. The arrangement of DS anions in the interlayer space of LZH-DS also depended on temperature. Remarkably, the basal spacing was considerably increased at 55 °C, which was explained by the formation of a second-staging heterostructure with the regular alternation of layers with two basal spacings, 31.5 and 34.2 Å. This is the first reported interstratification phenomenon in layered hydroxides intercalated with aliphatic molecules. Our results provide insight into the great variability of layered hydroxide structures controlled by external stimuli.