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The low temperature polycrystalline silicon (LTPS) method has proved to be a technical breakthrough, accomplishing semiconductor thin films with remarkable mobility for a range of high-performance displays, including liquid crystal display and organic light emitting diodes. However, utilizing a conventional excimer laser source for LTPS incurs high cost. In this paper, we demonstrate a comprehensive analysis of the crystallization mechanism of a-Si film (94 nm) and the thermal deformation of the glass substrate induced by Blue diode Laser Annealing (BLA). BLA provides high quality laterally grown crystals over 4 µm × 10 µm on glass substrates, which were examined by optical microscopy, scanning electron microscopy, and Raman spectroscopy. In addition, the permanent deformation introduced by the annealing process is numerically modeled, instantiating how to control the heat conduction from the thin film that affects the substrate. Our findings reveal that the permanent thermal deformation depth that can be obtained is comparable to the roughness of the silicon film for the optimum scanning speed and laser power. The combination of both experimental and numerical results elucidates the manifested physical mechanisms during the BLA process and provides the guidelines to improve the experimental parameters of this process.