Phase separation and viscoelastic effect play important roles in the properties of mesoscopic fillers reinforced polyethersulfone/cyanate ester composites. In this article, the effects of size and content of mesoscopic fillers on the polymerization induced viscoelastic phase separation of thermoplastic modified thermosets have been studied by using optical microscopy (OM), time-resolved light scattering (TRLS) and rheological instrument. The results of OM and TRLS showed that the characteristic length scale of phase structure of fillers added systems tended to shrink; while the relaxation time of phase separation increased with the decrease of filler size and enlargement of filler content. Rheological behaviours of blends filled with various types and contents of mesoscopic fillers are consistent with the phase separation process. The change of morphology and phase separation process was attributed to the significant enhanced viscoelastic effect of mesoscopic fillers. Both the tensile properties and toughness of cyanate ester blends have been improved due to the “enhanced viscoelastic effect” through addition of mesoscopic fillers. However, the “enhanced viscoelastic effect” of fillers almost disappeared with the diminishing of viscoelastic effect during phase separation.