We synthesized a series of acceptor-donor-acceptor type small-molecules (SIDPP-EE, SIDPP-EO, SIDPP-OE and SIDPP-OO) consisting of a dithienosilole (SI) electron-donating moiety and two diketopyrrolopyrrole (DPP) electron-withdrawing moieties each bearing linear n-octyl (O) and/or branched 2-ethylhexyl (E) alkyl side chains. X-ray diffraction patterns revealed that SIDPP-EE and SIDPP-EO films were highly crystalline with pronounced edge-on orientation, whereas SIDPP-OE and SIDPP-OO films were less crystalline with a radial distribution of molecular orientations. Near edge X-ray absorption fine structure (NEXAFS) spectroscopy disclosed an edge-on orientation with a molecular backbone tilt angle of ~22° for both SIDPP-EE and SIDPP-EO. Our analysis of the molecular packing and orientation indicated that the shorter 2-ethylhexyl groups on the SI core promote tight π-π stacking of the molecular backbone, whereas n octyl groups on the SI core hinder close π-π stacking to some degree. Conversely, the longer linear n-octyl groups on the DPP arms facilitate close intermolecular packing via octyl-octyl interdigitation. Quantum mechanics/molecular mechanics molecular dynamics (QM/MM MD) simulations determined the optimal 3-dimensional (3-D) positions of the flexible alkyl side chains of the SI and DPP units, which elucidates the structural cause of the molecular packing and orientation explicitly. The alkyl-chain dependent molecular stacking significantly affected the electrical properties of the molecular films. The edge-on oriented molecules showed high hole mobilities in organic field effect transistors, while the radially oriented molecules exhibited high photovoltaic properties in organic photovoltaic cells. These results demonstrate that appropriate positioning of alkyl side chains can modulate crystallinity and molecular orientation in SIDPP films, which ultimately have a profound impact on carrier transport and photovoltaic performance.