Janus rods due to their amphiphilic nature are highly attracted to the interface and their shape anisotropy results in formation of different self-assembled structures when they are incorporated into multi-phase systems. Their self-assembly can be manipulated for fabrication of engineered materials with superior properties. Thus we have performed numerical simulations namely, Dissipative Particle Dynamics, to investigate the influence of individual parameters that control Janus rods assembly at the interface of binary blends of immiscible polymers. In particular, we have studied the effect of interfacial orientation and aggeregation of Janus rods on the phase separation process when added to a polymer blend. Moreover, because flow can dramatically alter the localization of these particles within the polymer blend, we monitored not only the microstructures formed by these systems at rest, but we also did so under flow conditions and upon relaxation after flow cessation. We verified in our simulations various stabilizing effects provided by Janus rods depending on their configuration at the interface. The reversible responsive nature of Janus aggregates to shear flow and flow cessation is also useful to tune the final characteristics and properties of nano-composites by interfacial reconfigurable assembly. Therefore, We also studied the Janus aggregate-breakup process during shear and how these interfacial aggregates rebuild upon flow cessation. The results of this study can be used for designing new approaches for directing nano-particles into desired morphologies to achieve properties required for particular applications.