Due to the well-known significant effect of the size on the catalytic activity of nanocatalysts, here we use single-molecule fluorescence microscopy to study the size-dependent catalytic kinetics and dynamics of individual Pd nanocubes. A series of size-dependent catalytic properties were revealed in both product formation and product desorption processes. It was found that, due to the different adsorption mechanisms of substrate molecules on Pd nanocubes, H2 adsorption is independent of the size of Pd nanocubes, while the large flat resazurin molecules show stronger adsorption on larger sized Pd nanocubes. Apparently, the Pd nanocubes can be divided into three types: when the size of the Pd nanocube is small, substrate binding can prohibit product desorption and product desorption prefers the direct pathway; when the size is in an appropriate range, the product desorption process could be independent of substrate binding and shows no selectivity between two parallel desorption pathways; if the size is large enough, substrate binding can promote product desorption and product desorption prefers the indirect pathway. We also observed the surface-restructuring-induced dynamic heterogeneity of individual Pd nanocubes in both product formation and desorption processes with timescales of about tens to one hundred seconds. The activity fluctuation of individual Pd nanocubes was found to be mainly due to the spontaneous surface-restructuring rather than the catalysis. Furthermore, we estimated the size-dependent activation energies and time scales of spontaneous dynamic surface restructuring, which are fundamental to heterogeneous catalysis. The work presented here reveals new insight into nanocatalysis and exemplifies the advantages of the single-molecule approach in probing the catalytic properties of nanocatalysts.