Hydrogen has high energy density and is very attractive clean fuel, which is currently produced through stem reforming from hydrocarbons (fossil fuels), electrolysis and thermolysis of water, and biomass, etc. Direct water splitting is very attractive as a potentially environmentally clean process, however, it will not be clean in electrolysis and thermolysis processes if the power (electricity and heat) are from coal-burning power plants. On the other hands, direct solar water splitting using photoelectrochemical (PEC) cells promises cost-effective and carbon emission free hydrogen generation and has attracted a lot of interests. The semiconductor photoelectrodes are paramount to the PEC cell performance and hydrogen generation efficiency, and key parameters to consider in design are broad absorption spectrum and effective light absorption, effective charge transfer and energy band matching to H2 and O2 energy levels, long-term stability, and high photocurrent (for high photo-to-hydrogen conversion efficiency). Moreover, low-cost materials and easy to fabricate and scale up the photoelectrodes are also important for practical applications. Recently, we have demonstrated a 3-D branched nanowire heterostructures consisting of Si nanowire cores and ZnO nanowire branches, which offer the tunable and optimal properties for efficient light absorption due to light trapping effect, enhanced charge separation, large surface area, and show great promise in high efficiency for PEC electrodes. In addition, this 3-D branched ZnO/Si heterostructure is synthesized by a cost-effective and low-temperature solution based method. In this paper, we report an optimization of cell performance for this unique 3-D structures, particularly with consideration on the three important factors (absorption, photocurrent, and stability). By detail study of different branched structures using various etching and growth times, we show that smaller ZnO nanowire branches on Si nanowire cores provide higher absorption. This can also be confirmed by the change of sample’s color with different ZnO nanowire growth times. The photocurrent of diverse 3-D branched heterostructures is compared and optimized, and we demonstrated that smaller ZnO nanowires on longer Si nanowires present larger photocurrent under the illumination due to higher absorption and increased surface area for chemical reactions. Photocurrent variations versus potential are similar to those reported for TiO2 coated n-Si nanowire arrays. Furthermore, the cell stability (photocurrent measurement as a function of time in electrolyte) of different branched heterostructures is studied.