To develop high-performance nanostructured metal oxide electrodes, it is important to understand the structural effects on electrochemical performances. Thus, the preparation of metal oxide materials which have well-tailored nanostructures is crucial for the studies. However, while the synthetic strategies to control the size of metal oxide nanoparticles are well-developed, the control of those higher level structures, namely microstructure, is not established very well. Herein, we present the synthesis of two kinds of Co3O4 nanomaterials through pseudomorphic conversion that the macroscopic morphologies of parent MOFs such as plate-like and rod-like shape were well-maintained. Both Co3O4 nanomaterials are composed of almost identical 10 nm-sized primary nanocrystals, but those nanoporous secondary structures and macroscopic morphologies such as plate and rod shapes are different. Those Co3O4 nanomaterials were utilized as an electrode of lithium ion batteries (LIBs), and their electrochemical properties were comparatively studied. It was revealed that the different cyclability and rate capability is attributed to their different microstructures. Pseudo-monolithic integration of the primary and secondary structures at higher level was the governing factor to determine the electrochemical performances of the Co3O4.