It is well-known that photo-induced energy transfer and charge transfer (CT) are one of key factors for determining the device performances in the light harvesting systems and organic photovoltaics. These photophysical properties are closely related to the molecular microstructures and stacking arrangements, and finding the structure-property relationship thus becomes extremely important. Experimentally, a variaty of techniques have been proposed to regulate the intermolecular packing arrangement to improve the device efficiency, such as modulating the substitution positions, increasing the lengths of chains or directly adopting the highpressure technique. To microscopically reveal the underlying correlations between properties and stacking structures, one further requires electronic structure calculations and photo-induced carrier dynamic simulations. Dipyrrolonaphthyridinedion (DPND) has a series of cross-conjugated skeletons composed of electron-rich pyrrole rings and electron-poor carbonyl moieties, and is a kind of effective singlet fission materials with exceptional photophysical properties such as suitable energy level, good stability, high fission efficiency and adjusting molecular structures. The two DPND molecules, one with (DPND6) and the other without (DPND) alkyl side chains, exhibit the quite different photophysical properties in thin films, especially in the spectral characteristics and dynamics processes. For instance, the DPND thin film with the H-type aggregation has an accelerated singlet fission process compared to the DPND6 thin film, and the faster singlet fission process in DPND is attributed to the formation of a CT/excimer mixed state, in which the CT state is close in energy with Frenkel exciton (FE) and excimer states, which could drive excited-state population escaping from excimer trap and promote an ultrafast and highly efficient singlet fission process.