In two-dimensional magnets, the ultrafast photoexcited method represents a low-power and high-speed method of switching magnetic states. Bilayer CrI3 (BLC) is an ideal platform for studying ultrafast photoinduced magnetic phase transitions due to its stacking-dependent magnetic properties. Here, by using time-dependent density functional theory, we explore the photoexcitation phase transition in BLC from the R- to M-stacked phase. This process is found to be induced by electron-phonon interactions. The activated Ag and Bg phonon modes in the xy direction drive the horizontal relative displacements between the layers. The activated Ag mode in the z direction leads to a transition potential reduction. Furthermore, this phase transition can invert the sign of the interlayer spin interaction, indicating a photoinduced transition from ferromagnet to antiferromagnet. This investigation has profound implications for magnetic phase engineering strategies.