As a new type of photoelectrochemical technologies, photocatalytic fuel cell (PFC) based on optofluidics is a promising way to provide environmental protection and generate renewable energy simultaneously. However, large-scale application of the PFC technology is hampered by its low operating current density. Here we present a theoretical model to investigate the irreversible loss in optofluidic fuel cell (OFC). Experiments have been carried out to support the theoretical analysis. Results indicate that charge transfer either within semiconductor or at the interface of semiconductor/electrolyte can be the limiting step of OFC under different circumstances and the performance of OFC is determined by the dual-limiting mechanism. The model provides a comprehensive understanding of photoelectrochemical system and offers guidelines for future research in this area.