We have designed and synthesized a series of Schiff base derivatives, and studied their structural features in two-dimensional (2D) and three-dimensional (3D) states by combining scanning tunneling microscopy (STM) and X-ray diffraction experiments. The Schiff-base derivatives with short alkyl chains crystallize easily, which allows a detailed structural analysis by X-ray diffraction. Due to the strong adsorbate-substrate interactions, those bases with long alkyl chains easily form 2D assemblies on highly oriented pyrolytic graphite (HOPG). The STM images indicate also that the introduction of two methoxy groups into the molecule can change the structure of these 2D assemblies as a result of the increased steric hindrances, for example: the Schiff-base derivative, bearing both methoxy groups and C16H33 tails, forms 2D Moiré patterns, and an alignment of pairing Schiff-base molecules may be easily resolved. Conversely, the Schiff base derivative, bearing solely C16H33 tails, forms 2D non-Moiré patterns. It is demonstrated that the 3D structural features result from the compromise of intermolecular interactions of different molecular moieties. However, there is one more factor, which also governs the 2D structure: the adsorbate-substrate interaction. The 3D crystal structure may thus help to understand many factors involved in the formation of 2D structures, and would be helpful for designing new molecular assemblies with tailoring functions.