To study the mechanism of stimulated Brillouin scattering (SBS) excited by high energy laser in water, a structure model of a non-uniform refractive index grating based on nonlinear polarization and nonlinear absorption of high intensity laser is proposed, and the physical mechanism and spectral characteristics of SBS in water are analyzed. The mechanism of the non-uniform refractive index grating generated by SBS effect in water is studied by establishing the modulation structure and periodic structure of the non-uniform refractive index grating. The effect of the structure of the non-uniform refractive index grating on the spectral characteristics of SBS, such as linewidth, frequency shift, and diffraction efficiency, is analyzed by using the transfer matrix method. Also, the theoretical simulation results are compared with the experimental results. The results indicate that the theoretical simulation results are in good agreement with the experimental results, and the physical mechanism of SBS in water can be analyzed effectively by using the structure model of the non-uniform refractive index grating.