As a result of complex pore-throat geometry and precursor corner flow, the snap-off of the non-wetting phase occurs during the spontaneous imbibition (SI) of wetting phase. However, accurate modeling of such pore-scale flow behavior remains a big challenge, and its influencing factors remain unclear. In this study, an improved pseudopotential lattice Boltzmann method (LBM) is used to analyze the snap-off behavior during the SI process in three-dimensional (3D) pore-throat models with rough surfaces. The influence of the pore-to-throat size ratio (λ), contact angles (θ), and Ohnesorge number (Oh) on the occurrence of the snap-off are investigated and based on which a 3D phase diagram is established. The snap-off is more likely to occur with the increase in λ and Oh and decrease in θ, respectively. Only when the λ is ≥2 and the θ is <13°, the snap-off may occur. With the increase in θ from 0° to 13°, the snap-off is suppressed due to the relatively small advancing difference between the corner flow and the bulk meniscus. Volume fraction of the entrapped gas bubble in the pore increases with the increase in λ and Oh and the decrease in θ. The time when snap-off occurred increases with the increase in λ and θ, and decrease in Oh. These results are fundamental for investigating snap-off phenomena in real 3D pore space and guide how to avoid or facilitate the occurrence of snap-off and to control the degree of snap-off.