The conformation of embedded molecule in a polymer matrix is sensitive to the local nano-environment that the molecule experiences. Particularly, single molecule spectroscopic methods have been utilized to visualize each molecular conformation in local sites of the polymer matrix by monitoring rotational diffusion and fluctuating fluorescence of the molecule. Here, we have performed single molecule spectroscopic experiments on a π-stacked perylenediimide (PDI) dimer and trimer, in which enhanced π-π interaction in π-stacked PDIs makes the fluorescence lifetime longer, embedded in two different polymers, namely poly(methyl methacrylate) (PMMA) and poly(butyl methacrylate) (PBMA), to reveal the conformational change depending on the polymer matrix. The fluorescence lifetimes of π-stacked PDIs are influenced by polymer surroundings because their molecular conformations are dependent on their interactions with the local environment in the polymer matrix. Furthermore, from an in-depth analysis of autocorrelation functions of fluorescence intensity trajectories, we could assign that the first autocorrelation value (lag 1) is larger as the intensity trace becomes more fluctuating. Thus, we expect that π-stacked PDIs, a model system for the formation of PDI excimer-like states, can be utilized to probe the surrounding nano-environment by monitoring the conformational change in real time.