The assembly of nanoparticles into ordered 3D architectures, which requires more complex spatial arrangements of nanoparticles than 2D, is essential to develop new nano- or microdevices in the fields of biotechnology, magnetic devices, catalysis, and optoelectronics. However, because of the long-distance interactions among the nanoparticles or the applied external force, the movement of nanoparticles cannot be precisely controlled, particularly in multidimensional architectures. Therefore, controlling the 3D architecture remains challenging. In this study, the 3D architecture engineering of colloidal particles by manipulating the microfluid morphology is reported, which produces controllable cross-sections and shapes. The modification of the microfluid morphology, which can be achieved by tuning the physical parameters of the system and the pinning point number, affects the nucleation location, growth rate, and orientation of the architectures. Because of the controllable morphology, the waveguiding distance and direction of 3D architectures can be manipulated. Thus, this study highlights the opportunity for creating morphology-controlled 3D architectures with potential applications in optoelectronics.