Multiwalled carbon nanotubes (MWCNTs) that were treated with mixed acids were used to reinforce the cyanate ester resin. Meanwhile, the relationship among structure, morphology, and property of the modified resin was investigated. The treated MWCNTs were characterized by Fourier transform infrared spectroscopy (FTIR), thermogravimetric analysis, and X-ray photoelectron spectroscopy (XPS). The XPS results showed that the oxygen content in the treated MWCNTs was higher than that of untreated MWCNTs and the FTIR results indicated the presence of oxygen-containing functional groups on the treated MWCNTs. The microstructure of the resin was characterized by scanning electron microscopy and transmission electron microscopy. The results showed that the dispersion properties of the treated MWCNTs in the resin matrix were improved and compared with the untreated analogue. Addition of MWCNTs to the resin had little effect on the thermodynamic properties of the resin system. Upon addition of 0.8 wt% of MWCNTs to the resin, the glass transition temperature of the cured resin changed from 298°C to 285°C, maintaining a relatively high value. For the resins containing 0.6 wt% of treated MWCNTs, the plane strain critical stress intensity factor and plane strain critical strain energy release rate in the system were determined to be 1.39 Pa·m0.5 and 364 J m−2, respectively, and the fracture toughness is increased by 45.7 and 76.0%, respectively. Furthermore, the modified resin system exhibits excellent toughness and thermal properties. Therefore, the modified resin may be suitable for future applications involving high performance composites and adhesives.