Construction of macro-materials with highly oriented microstructures and well-connected interfaces between building blocks is significant for a variety of applications. However, it is still challenging to confine the desired structures. Thus, well-defined building blocks would be crucial to address this issue. Herein, we present a facile process based on 1.8 nm Pd nanoclusters (NCs) to achieve centimeter-size assemblages with aligned honeycomb structures, where the diameter of a single tubular moiety is ∼4 μm. Layered and disordered porous assemblages were also obtained by modulating the temperature in this system. The reconciled interactions between the NCs were crucial to the assemblages. As a comparison, 14 nm Pd nanoparticles formed only aggregates. This work highlights the approach of confining the size of the building blocks in order to better control the assembly process and improve the stability of the structures. [Figure not available: see fulltext.].