Janus particles are highly active at the interface of immiscible fluids and thus they can self-assemble into different structures when incorporated into multiphase systems. In the case of Janus rods, their anisotropy and amphiphilic nature result in superior properties and their self-assembly can be manipulated for fabrication of engineered materials. The structures formed by the Janus rods can be tuned by varying different parameters in the system. Therefore, understanding the effect of the deterministic factors on Janus rod self-assembly is of crucial importance and has the potential to pave the way for designing new functional materials. Herein, we perform mesoscale simulations in order to investigate the influence of individual parameters on the structures formed by Janus rods at the interface of two immiscible liquids. In particular, Dissipative Particle Dynamics simulations are performed to explore the effect of Janus structure and interface properties on the self-assembled structures. Janus rods exhibit varying orientational preferences at the interface and ultimately, these particles are incorporated into binary blends of immiscible polymers. The interfacial orientation and self-assembly of Janus rods are shown to be highly influential in controlling the phase separation process when added to a polymer blend. Moreover, flow can dramatically alter the localization of these particles within the polymer blend. Therefore, we not only monitor the microstructures formed by these systems at rest, but we also do so under flow conditions and upon relaxation after flow cessation. The results of this study can be used for designing new approaches for directing nano-particles into desired morphologies, which will subsequently tune the final characteristics and properties of nano-composites.