The correlation between molecular structure and its photophysics is well reported, and organic chemistry is blessed with the freedom of substitution to obtain the desired photophysical property, suitable to control the functional aspects of materials. Despite the fact that the photodynamics of perylene has been studied in depth, its bay and peri aryl-substituted derivatives have not been studied to that extent. Herein, the ultrafast photo-dynamics of two anisyl perylene derivatives (peri-OCH3 and bay-OCH3) is presented. Isomers of anisyl perylene were designed to study the positional effect of substitution on their molecular packing and excited-state photophysics. The fluorescence spectra of nanoaggregates of peri-OCH3 showed excimer formation, while monomer emission is dominated in bay-OCH3. These features are consistent with the solid-state α-phase and β-phase of perylene, respectively, which are grown in a very precise and controlled manner. Excited-state dynamics studies show that in peri-OCH3, the monomeric free excitons undergo a relatively faster decay to populate the self-trapped monomeric excitonic state and E-state. In bay-OCH3, the contribution of emission from the Y-state and E-state is much less. The molecular structure alteration and different packing are also observed to have an impact on the exciton diffusion rate. The bay-OCH3 isomer is observed to have an almost-double diffusion length, which is attributed to the slightly faster diffusion and longer lifetime of free excitons. The present report indicates the structural modulation effect on the exciton-to-excimer transition dynamics and exciton diffusion properties, which can be bene ficial in designing perylene-based materials for organic electronics.