Structurally flexible organic porous molecular arrays are promising for the development of vapochromic materials with superior detection performance. Exploring the photophysical control of vapochromic materials using these molecular arrays is important for the design of new vapochromic materials. However, difficulties arise in the formation and control of organic porous molecular arrays owing to weak and less‐oriented noncovalent forces and their tendency to arrange into energetically preferred high‐density configurations. Herein, an efficient strategy is presented to control molecular arrays by manipulating the shapes of donor–acceptor–donor system‐based molecular building blocks using positional isomerism and report on the correlation between controlled molecular arrays and vapochromic behavior. Depending on their shape (Z‐shaped, quasi‐Z‐shaped, or linear shape), the building blocks formed different molecular arrays that controlled the intermolecular interactions and void volumes. This led to differences in the final microstructural morphologies. Consequently, they exhibited different vapochromic behaviors, and an in‐depth understanding of the correlation between the molecular arrays and vapochromism/vapofluorochromism is obtained.