A novel modification of cyanate ester (CE) resin by epoxidized polysiloxane (E-Si) has been developed, and the modified system is coded as CE/E-Si. E-Si was prepared by the reactions among octamethylcyclotetrasiloxane, hexamethyldisiloxane, (3-aminopropyl)-methyldiethoxysilane, and diglycidyl ether of bisphenol-A resin. Six formulations were designed to evaluate the effect of the weight ratio between CE and E-Si on performance parameters. Results reveal that the addition of E-Si in CE resin cannot only significantly decrease the curing temperature of the CE resin but also improve the water resistance and toughness of original CE resin. Moreover, these positive effects increase with the increase of E-Si concentration in CE/E-Si systems. Thermal property investigation shows that the glass-transition temperature and initial degradation temperature of CE/E-Si systems are lower than that of original CE resin. For the flexural properties of the CE/E-Si systems, the E-Si concentration in the system exists a threshold, that is, when the E-Si concentration is smaller than the threshold, original CE and CE/E-Si systems have similar flexural properties, whereas when the E-Si concentration is higher than the threshold, CE/E-Si systems have lower flexural properties than original CE resin. All these changes of properties are closely correlated to the structure alteration from neat CE to CE/E-Si networks.