The high-precision deposition of highly crystalline organic semiconductors by inkjet printing is important for the production of printed organic transistors. Herein, a facile nonconventional lithographic patterning technique is developed for fabricating banks with microwell structures by inkjet printing solvent droplets onto a polymer layer, thereby locally dissolving the polymer to form microwells. The semiconductor ink is then inkjet-printed into the microwells. In addition to confining the inkjet-printed organic semiconductor droplets, the microwells provide a platform onto which organic semiconductor molecules crystallize during solvent evaporation. When printed onto the hydrophilic microwells, the inkjet-printed 6,13-bis(triisopropylsilylethynyl) pentacene (TIPS_PEN) molecules undergo self-organization to form highly ordered crystalline structures as a result of contact line pinning at the top corner of the bank and the outward hydrodynamic flow within the drying droplet. By contrast, small crystallites form with relatively poor molecular ordering in the hydrophobic microwells as a result of depinning of the contact line along the walls of the microwells. Because pinning in the hydrophilic microwells occurred at the top corner of the bank, treating the surfaces of the dielectric layer with a hydrophobic organic layer does not disturb the formation of the highly ordered TIPS_PEN crystals. Transistors fabricated on the hydrophilic microwells and the hydrophobic dielectric layer exhibit the best electrical properties, which is explained by the solvent evaporation and crystallization characteristics of the organic semiconductor droplets in the microwell. These results indicate that this technique is suitable for patterning organic semiconductor deposits on large-area flexible substrates for the direct-write fabrication of high-performance organic transistors.