Polybenzoxazines are emerging as a class of high-performance thermoset polymers that can find their applications in various fields. However, its practical application is limited by its low toughness. The cyclic β-cyclodextrin and a newly synthesized derivative (β-cyclodextrin-MAH) were separately blended with benzoxazine to improve the toughness of polybenzoxazine. The results revealed that the maximum impact strength of the blend was 12.24 kJ·m−2 and 14.29 kJ·m−2 when 1 wt.% of β-Cyclodextrin and β-Cyclodextrin-MAH, respectively, were used. The strengths were 53% and 86% higher than that of pure polybenzoxazine. The curing reaction, possible chemical structures, and fractured surface were examined using differential scanning calorimetry, Fourier transform infrared spectroscopy, and scanning electron microscopy techniques to understand the mechanism of generation of toughness. The results revealed that the sea-island structure and the presence of hydrogen bonds between polybenzoxazine and β-cyclodextrin and β-cyclodextrin-MAH resulted in the generation of toughness. Furthermore, the curves generated during thermogravimetric analysis did not significantly change, revealing the good thermal properties of the system. The phase-separated structure and the hydrogen bonds present in the system can be exploited to prepare synergistically tough polybenzoxazine exhibiting excellent thermal properties. This can be a potential way of modifying the thermoset resins.