Organic-inorganic hybrid halide perovskites (ABX3), especially layered 2D perovskites, have been recognized as promising semiconductors due to their tunable crystal structure and the unique optoelectronic properties. A-site cations, as spacers, allow various metal halide assemblies, but the stacking pattern and the influence of their collective behavior on the properties of the resultant materials remain ambiguous. Here, the cation stacking effects in the 2D perovskite single crystals, with the focus on the electron-phonon interaction is investigated. We reveal the different photoluminescence from the surface region and the interior of the crystal, which is owing to the residual strain induced by A-site cation stacking. We also examine the cation stacking effects on electron-phonon interaction, which is further employed to tailor the optoelectronic properties of the resultant 2D crystals. By reducing the microstrain, we reduce the electron-phonon coupling to improve the mobility and their stability against electric field in the corresponding crystals. Our study suggests a way to manipulate the optoelectronic properties in 2D perovskite materials by rational design of cation stacking.