The cooperative assembly of nanoparticles and amphiphilic molecules has emerged as an appealing strategy for fabricating hybrid nanomaterials for a wide range of potential applications. However, it is challenging to precisely manipulate hybrid nanostructures. In this study, extensive dissipative particle dynamics simulations are carried out to investigate the cooperative assembly of amphiphilic oligomers and triblock Janus nanoparticles with different hydrophobic-hydrophilic patches. Three different hybrid nanostructures (networks, disks, and vesicles) are observed from the simulations. The structural characteristics and kinetic pathways are analyzed in detail. We reveal that the hydrophobic-hydrophilic patches in the triblock Janus nanoparticles significantly affect the arrangement of amphiphiles and nanoparticles, as well as the orientational degree of freedom between nanoparticles; therefore, the triblock Janus nanoparticles can function as a robust structure-directing agent to regulate the spatial organization of nanoparticles in networks, the curvature of disks, and the size of vesicles. This study demonstrates the cooperative assembly can serve as an efficient platform for the engineering of hybrid nanomaterials with tailored nanostructures.