2D hybrid organic–inorganic perovskites (HOIPs) have great prospects in new-generation photovoltaic and luminescence applications. The complex interaction between exciton and lattice motions plays an important role in determining the exciton properties of 2D HOIPs. However, the exploration of the regulation mechanism of phonons and the exciton–phonon (ex–ph) interaction is still very limited, especially for Dion-Jacobson (DJ) type 2D HOIPs. Here, we investigate three DJ-type 2D HOIPs with different cations, (3AMP)PbI4, (4AMP)PbI4, and (1,6-HDA)PbI4, using temperature-dependent steady-state spectra and time-resolved spectra. It is found that the subtle difference of functional group position in cations and the difference between ring and straight carbon chains have a profound effect on the structural distortion, the ex–ph coupling strength, and even the band gap variation trend with temperature in the DJ type 2D HOIP system. The study provides new insights into how to manipulate ex–ph interactions by targeting ligand modifications to 2D perovskite structures.