Polymer blend compatibilization is a well-known way to mix different polymers and obtain desired material properties that would not be obtainable separately with each polymer. In recent years, Janus-like nanoparticle surfactants have been praised to be the next generation of polymer blend compatibilizers in view of their enhanced interfacial activity and they have also been found to outperform block co-polymer compatibilizers in reducing interfacial tension. In the case of Janus rigid surfactants, both shape and chemical anisotropy within the same particle offer a way to control particle orientation and self-assembly at the interfacial level. However, the aggregation behavior of such Janus particles under shear flow and their relaxing behavior is far from being well-understood. Studying the effect of flow and its cessation as a tool of external manipulation/actuation in soft metamaterial systems is important for fine-tuning the microstructure and may pave the way for the design of smart nanodevices. In the present work, Dissipative Particle Dynamics is used as a way to computationally assess how Janus nanorods assemble at the interface of immiscible binary polymer blends. A very rich behavior has been verified consisting of tilting, tumbling and Janus aggregate break-up at a flat interface between two polymer phases and Janus aggregates have been also found to rebuild upon flow cessation. The results highlight the interplay between hydrodynamic and capillary torques on the particles at the interface and, depending on the direction of the interface normal with respect to the velocity-gradient direction, different self-assembled structures form at the interface. The results additionally shed light on the potential of using shear flow to nanoscopically engineer interfacial structure and on what the consequences could be for resulting nanoparticle orientation at the interface after polymer processing operations, for example.