The toughness of polycyanate ester is improved by adding epoxy pre‐polymer with varying molecular weights. The curing mechanism of epoxy prepolymer (PreEP) and cyanate ester (CE) is discussed based on differential scanning calorimeters and Fourier‐transform infrared spectroscopy. The mechanical, phase separated structures and thermal properties of PreEP/CE are also evaluated. It is found that the molecular weight of PreEP can reach 1,800 when it is cured at 90°C for 45 min by using a set amount of polyetheramine. Meanwhile, by increasing the molecular weight of the prepolymer, the mechanical properties of PreEP/CE show increased first, and then decreased. 0.2 PreEP/CE has the highest bending strength and impact strength (105.8 MPa and 18.3 kJ·m−2). There are 26.7 and 114.5% higher than those of polycyanate ester, respectively. The tougher PreEP/CE is attributable to the phase‐separated structures and the decrease in the cross‐linked product (Oxazolidinone) in PreEP and CE. The method showed in this article provides a new way to improve the toughness properties of thermoset resin.