Organic–inorganic halide perovskites incorporating two-dimensional (2D) structures have shown promise for enhancing the stability of perovskite solar cells (PSCs). However, the bulky spacer cations often limit charge transport. Here, we report on a simple approach based on molecular design of the organic spacer to improve the transport properties of 2D perovskites, and we use phenethylammonium (PEA) as an example. We demonstrate that by fluorine substitution on the para position in PEA to form 4-fluorophenethylammonium (F-PEA), the average phenyl ring centroid–centroid distances in the organic layer become shorter with better aligned stacking of perovskite sheets. The impact is enhanced orbital interactions and charge transport across adjacent inorganic layers as well as increased carrier lifetime and reduced trap density. Using a simple perovskite deposition at room temperature without using any additives, we obtained a power conversion efficiency of >13% for (F-PEA)2MA4Pb5I16-based PSCs. In addition, the thermal stability of 2D PSCs based on F-PEA is significantly enhanced compared to those based on PEA.