Supercapacitor is a promising electrochemical storage system simultaneously having high energy density and high power density. Its performance is significantly affected by electrode materials and the materials’ size, morphology, aggregation state and hierarchical nanostructure which have an effect on electrolyte transportation. Here, the influence of morphology on the capacitive performance of supercapacitor is studied by using polypyrrole (PPy) nanomaterials as model materials. PPy with different morphologies (separated nanodots, vertically aligned nanorods, nanowires and nanomats assembled by random fallen nanowires) are electrodeposited on graphite rods (GR) by potentiostatic polymerization method. The capacitance performance of these prepared PPy/GR electrodes is investigated by cyclic voltammetry (CV) and galvanostatic charge/discharge methods, which exhibits ideal pseudo-capacitance characteristics. Because of the electrolyte diffusion-controlled nature, the high capacitance performance of PPy/GRs can be attained by increasing the effective surface area of the electrode, elevating the test temperature, using high concentration electrolyte and intensifying the process of mass transfer. The experimental results demonstrate that supercapacitors fabricated with separated nanoparticles or vertically aligned nanowires have an ideal capacitor performance. Although the PPy nanomats prepared in this article also has high mass specific capacitances and area specific capacitances, their columbic efficiency becomes lower. To our best knowledge, this is the first report on the effect of morphology on the capacitance performance from the perspective of mass transfer, which gives some new insights on the fabrication of supercapacitor electrodes.