Understanding charge transfer (CT) in electron donor-acceptor systems is critical for the development of more efficient organic photovoltaics (OPVs). Donor-acceptor systems are what compose the active layer in OPVs, and when light is absorbed in the active layer, an electron-hole pair, or exciton, is generated. CT takes place at a donor-acceptor interface, resulting in the electron and hole residing in the acceptor and donor materials, respectively. If these charges can overcome their binding energy, they are able to move further apart, and the result is a charge separated state. CT character can be increased within individual molecules in donor-acceptor-donor (D-A-D) systems, wherein moieties within a single molecule can act as electron donors or acceptors. When organic molecules such as these are cast into films, a variety of molecular orientations are formed due to weak intermolecular forces. Molecules in orientations that yield lower energy excitonic states can act as exciton traps that may decrease the tendency for charge transfer or separation to occur. In this study, we aim to investigate the effects of thermal annealing on the prototypical electron donor-acceptor system, poly(3-hexylthiophene) (P3HT): phenyl C61 butyric acid methyl ester (PCBM), and a squaraine D-A-D molecule, 2,4-bis(4-dihexylamino-2,6-dihydroxyphenyl) cyclobutene-1,3-dione (DHSQ(OH)₂). Films composing these molecules are often thermally annealed to change the morphology to form larger, more stable aggregates. Although spectroscopy can be used to characterize films before and after thermal annealing, this does not reveal the evolution of morphology or excited state dynamics during annealing. We performed in situ characterization during thermal annealing with a combination of linear and transient absorption measurements. A kinetic model and global fitting were applied to the transient absorption data for further interpretation of the excited state dynamics. Here we report on the evolution of exciton dynamics during thermal annealing of electron donor-acceptor systems to gain insight into how thermal annealing affects morphology and charge separation.