Epoxy‐cyanate ester blends have attracted significant attention due to their unique synergistic properties and versatility in high‐performance applications. However, achieving precise control over the phase‐separated structures in these blends remains a challenge. In this work, we present a strategy for the preparation of epoxy‐cyanate ester blends with high‐performance through staged curing‐induced phase separation. By incorporating a thermally latent catalyst, 4‐ethyl‐2‐methylimidazole tetraphenylborate, into the epoxy‐anhydride‐cyanate system, the reactivity differences of multiple curing reactions within the blend were precisely controlled, thereby inducing the formation of well‐defined nanophase‐separated structures. The polymer systems prepared exhibit high mechanical properties and heat resistance, primarily due to the interpenetrating networks created by the epoxy‐anhydride‐cyanate ester and the formation of nanodomains induced by the staged curing process. Furthermore, epoxy‐cyanate ester blends demonstrate outstanding hygrothermal resistance due to the low polarity of the crosslinked network structure. This work provides new insights into regulating the microstructure of the thermosetting blends and expands the potential applications of these materials in fields requiring long‐term durability and reliability.