The toughness of cyanate ester resin (CE) matrix was improved significantly with addition of carboxyl-randomized liquid butadiene-acrylonitrile rubber (CRBN). The curing behavior of the system was studied by differential scanning calorimetric (DSC) and Fourier transform infrared spectrum (FTIR). The results showed that carboxyl groups on the CRBN chain had slight activation effect to CE curing reaction at the beginning of the cure process. Phase separation was the main toughening mechanism for CE/CRBN composites. The existence of micro-size pores induced by small amount of the low weight molecular part of CRBN might be another toughening mechanism. The toughening mechanism was proved powerfully from the aspect of free-volume using positron annihilation lifetime spectroscopy (PALS). PALS is qualitatively sensitive to the existence of pores induced by low molecular weight part of CRBN during curing process.