Two-dimensional (2D) photocatalytic material is a vital project for modern solar energy conversion and storage. Despite a vast family of potential 2D photocatalysts that is demonstrated, their commercial applications are severely limited because of fast photogenerated electron-hole recombination. Here, based on first-principles, we propose a general paradigm to boost the separation of photoexcited charge carriers in 2D photocatalysts by stacking engineering. Taking the emerging water splitting photocatalyst MoSi2N4 as an example, we show that specific interlayer stacking-induced electric polarization plays a significant role in altering the electronic properties and thus the suppressed recombination rate of photoexcited carriers. Moreover, we find that the catalytic performance can be further controlled by vertical strain. These generalized findings not only highlight the importance of stacking-induced electric polarization but also offer new prospects for the design and application of 2D photocatalysts.