In this study, the effect of molecular features of guest molecules on the structure, property, and formation of poly(vinyl alcohol) (PVA)/beta-cyclodextrin (bCD) inclusion compound hybrid films was investigated using three types of guest molecules such as hydroquinone (HQ), arbutin (AB), and tranexamic acid (TA). First, the successful formation of inclusion compounds between bCD and the guest molecules, and polymer/inclusion compound hybrid were proved using Raman spectroscopy. The effect of bCD-based inclusion compounds on the structure and property of PVA matrix composites containing inclusion compounds was also studied using X-ray diffraction (XRD) and thermal analyses such as differential scanning calorimetry (DSC) and thermogravimetric analysis (TGA). It was notable that the effect of TA to the crystalline structure of the PVA was significantly different from that of using other guest molecules including HQ and AB. It was also supported by a simple molecular simulation result. This article will be a good example for demonstrating the effect of molecular characteristics on the inclusion compound formation in polymer films, which can provide important information for relevant future research.