Thermal expansion is a crucial factor for the performance of laser devices, since the induced thermal stress by laser irradiation would strongly affect the optical beam quality. For BaAlBO3F2 (BABF), a good non-linear optical (NLO) crystal, due to the highly anisotropic thermal expansion its practical applications are strongly affected by the “tearing” stress with the presence of local overheating area around the laser spot. Recently, the strategy to place the optical crystals in low-temperature environment to alleviate the influence of the thermal effect has been proposed. In order to understand the prospect of BABF for this application, in this work, we investigated its thermal expansion behavior below room temperature. The variable-temperature XRD showed that the ratio of thermal expansion coefficient between along c- and along a(b)- axis is high as 4.5:1 in BABF. The Raman spectrum combined with first-principles phonon analysis revealed that this high thermal expansion anisotropy mainly ascribe to progressive stimulation of the respective vibration phonon modes related with the thermal expansion along a(b)- and c-axis. The good NLO performance in BABF can be kept below room temperature. The work presented in this paper provides an in-depth sight into the thermal expansion behavior in BABF, which, we believe, would has significant implication to the manipulation in atomic scale on the thermal expansion of the materials adopted in strong-field optical facility.