Abstract The morphological and rheological responses to the transient and steady shear flow for a phase-separated polybutadiene (PB)/low vinyl content polyisoprene (LPI) blend have been investigated. Under steady shear flow where the applied shear rate is not too large, the steady sheared structures become increasingly anisotropic and interconnected with an “en route” to the formation of string phases as shear rate increases. After that, the further increase of shear rate leads to a blurred domain interface. These shear-induced complex structures in turn affect the rheological response greatly and both the shear thinning and shear thickening were observed in the steady shear behavior of the phase-separated PB/LPI blend. Under transient shear flow, the time (or strain) dependence of viscosity and morphology after a shear rate jump were extensively studied in order to obtain the insight into the steady state formation and found to be mainly determined by the final shear rates. Depending on whether the transient string phases which were formed by the transient shear flow can be stabilized and with clear domain interface, three kinds of transient shear viscosity changes have been observed. Some of the observations are quite different from the model immiscible blend and believed to be closely related to the significant shear-induced mixing effect happened in the PB/LPI blend.