Self-assembled colloidal patterns have been fabricated on a substrate using inkjet printing with an ink of submicron-sized monodisperse silica particles. The ink are prepared with well-dispersed suspension of monodisperse silica particles. Dot patterns are formed on both hydrophilic silicon wafer and hydrophobic silicon wafer modified with octadecyltrichlorosilane. It was found that the uniformity and spatial extent of the self-assembly within a dot were significantly influenced by the interaction of the ink with substrates and its drying behavior. For the improvement of pattern resolution, we treat a silicon wafer with OTS by a contact-printing. Chemically heterogeneous substrate has repeated stripe patterns of hydrophilic and hydrophobic properties with different relative widths. When jetting conditions are well controlled, we demonstrate to directly print the line pattern with the width of 21 μm, which is difficult to achieve by the conventional ink-jet printing. The internal and external structures of the colloidal aggregates were observed by scanning electron microscope (SEM) and confocal microscopy.