Transparent glass-ceramics with a Li₂O–Al₂O₃–SiO₂ (LAS) system have been extensively utilized in optical systems in which thermal stability is of utmost importance. This study is aimed to develop thermal treatment routes that can effectively control the structure of transparent LAS glass-ceramics and tune its thermal expansion coefficient within a wide range for novel applications in photonics and integrated optics. The optimal conditions for the nucleation and crystallization of LAS glass were determined by means of differential scanning calorimetry and a polythermal analysis. XRD, Raman spectroscopy, and TEM microscopy were employed to examine the structural changes which occurred after heat treatments. It was found that the second stage of heat treatment promotes the formation of β-eucryptite-like solid solution nanocrystals, which enables effective control of the coefficient of thermal expansion of glass-ceramics in a wide temperature range of −120 to 500 °C. This work provides novel insights into structural rearrangement scenarios occurring in LAS glass, which are crucial for accurately predicting its crystallization behavior and ultimately achieving transparent glass-ceramics with desirable properties.