The assembly of artificial nano- or microstructured materials with tunable functionalities and structures, mimicking nature's complexity, holds great potential for numerous novel applications. Despite remarkable progress in synthesizing colloidal molecules with diverse functionalities, most current methods, such as the capillarity-assisted particle assembly method, the ionic assembly method based on ionic interactions, or the field-directed assembly strategy based on dipole-dipole interactions, are confined to focusing on achieving symmetrical molecules. But there have been few examples of fabricating asymmetrical colloidal molecules that could exhibit unprecedented optical properties. Here, we introduce a microfluidic and magnetic template-assisted self-assembly protocol that relies mainly on the magnetic dipole-dipole interactions between magnetized magnetic-plasmonic nanoparticles and the mechanical constraints resulting from the specially designed traps. This novel strategy not only requires no specific chemistry but also enables magnetophoretic control of magnetic-plasmonic nanoparticles during the assembly process. Moreover, the assembled asymmetrical colloidal molecules also exhibit interesting hybridized plasmon modes and produce exotic optical properties due to the strong coupling of the individual nanoparticle. The ability to fabricate asymmetrical colloidal molecules based on the bottom-up method opens up a new direction for the fabrication of novel microscale structures for biosensing, patterning, and delivery applications.