Despite rapid improvements in efficiency, long-term stability remains a challenge limiting the future up-scaling of perovskite solar cells (PSCs). Although several approaches have been developed to improve the stability of PSCs, applying ammonium passivation materials in bilayer configuration PSCs has drawn intensive research interest due to the potential of simultaneously improving long-term stability and boosting power conversion efficiency (PCE). This review focuses on the recent advances of improving n-i-p PSCs photovoltaic performance by employing ammonium halide-based molecular modulators. The first section briefly summarizes the challenges of perovskite materials by introducing the degradation mechanisms associated with the hygroscopic nature and ion migration issues. Then, recent reports regarding the roles of overlayers formed from ammonium-based passivation agents are discussed on the basis of ligand and halide effects. This includes both the formation of 2D perovskite films as well as purely organic passivating layers. Finally, the last section provides future perspectives on the use of organic ammonium halides within bilayer-architecture PSCs to improve the photovoltaic performances. Overall, this review provides a roadmap on current demands and future research directions of molecular modulators to address the critical limitations of PSCs, to mitigate the major barriers on the pathway toward future up-scaling applications.