To further understand the relationship among molecular conformational flexibility, thermodynamics, nucleation, and the polymorphic outcomes, the homogeneous nucleation and heterogeneous nucleation from fast cooling crystallization, evaporative crystallization, antisolvent crystallization, and solution-mediated polymorphic transformation were studied, considering the effects of temperature, supersaturation, and solvent. The conformers can rapidly fluctuate in solution with either monomers solvated by solvent molecules or carboxylic acid dimers and stacked dimers. No links between conformational flexibility and polymorphic outcome were found from both the experiment results and DFT calculation, though conformational polymorphs were obtained during the crystallization of 4-hexyloxybenzoic acid (HOBA). The stability relationship of HOBA polymorphs was confirmed, and the desolvation process was found to play a vital role in the overall self-assembly during crystallization. Finally, a process-control chart to prepare different polymorphs of HOBA was drawn to summarize the polymorphic differences caused by conformation.