A new type of atropisomerism has recently been discovered in 1,3-benzoxazines, where the intramolecular repulsion between negatively charged oxygen atoms on the imide and the oxazine ring hinders the rotation about the C–N bond. The imide group offers a high degree of flexibility for functionalization, allowing a variety of functional groups to be attached, and producing different types of end-caps. In this work, the effects of end-caps on the atropisomerism, thermally activated polymerization of ortho-imide functional benzoxazines, and the associated properties of polybenzoxazines have been systematically investigated. Several end-caps, with different electronic characteristics and rigidities, were designed. 1H and 13C nuclear magnetic resonance (NMR) spectroscopy and density functional theory (DFT) calculations were employed to obtain structural information, and differential scanning calorimetry (DSC) and in situ Fourier transform infrared (FT-IR) spectroscopy were also performed to study the thermally activated polymerization process of benzoxazine monomers. We demonstrated that the atropisomerization can be switched on/off by the manipulation of the steric structure of the end-caps, and polymerization behaviors can be well-controlled by the electronic properties of the end-caps. Moreover, a trade-off effect were found between the thermal properties and the rigidity of the end-caps in polybenzoxazines.