Tuning the microstructures of electrodes plays a vital role in enhancing the electrochemical performance of supercapacitors. In this work, we have developed a simple and effective way to tune the microstructures of graphene-based electrode by assembling different sizes of graphene sheets under vacuum filtration and freeze drying. It is found that the large-sized reduced graphene oxide (RGO) sheets (e.g., RGO-50) are assembled in large and nearly parallel structures showing poor capacitive performance due to the long transfer length of electrolyte ions in the layered structure, while the RGO film with small-sized RGO sheets (e.g., RGO-8000) has relatively small pores, thus showing low capacitance on account of low electrical conductivity. The RGO film with moderate RGO sheets shows proper porous and honeycomb-like network and thus has the largest capacitance (260.2 F g(-1)), ascribed to the balance of electrical conductivity, ion diffusion and reaction interface. By considering their microstructures, a theoretical model is developed which can describe the electrical conductivity of RGO films assembled by different sizes of RGO sheets. The results presented herein exploring structure-capacitance relation of graphene-based electrode may provide useful insight for designing high-performance energy storage devices.