Silicon nanowire (SiNW) arrays are widespread applied on hybrid photovoltaic devices because SiNW arrays can substitute the pyramid texture and anti-reflection coating due to its strong light trapping. Also, SiNWs can be prepared through a cost-efficient process of metal-assisted chemical etching. However, though longer SiNW arrays have lower reflectance, the top of long SiNWs aggregate together to make junction synthesis difficult for SiNW/organic hybrid solar cell. To control and analyze the effect of SiNW array morphology on hybrid solar cells, here we change the metal deposition condition for metal-assisted chemical etching to obtain different SiNW array morphologies. The experiment was separated to two groups, by depositing metal, say, Ag, before etching (BE) or during etching (DE). For group BE, Ag was deposited on n-type Si (n-Si) wafers by thermal evaporation; then etched by H2O2 and HF. For group DE, n-Si was etched by Ag+ and HF directly. Ag was deposited on n-Si during etching process. Afterwards, residual Ag and SiO2 were removed by HNO3 and buffered HF, successively; then Ti and Ag were evaporated on the bottom of Si to be a cathode. Finally, SiNWs were stuck on the poly(3,4-ethylenedioxythiophene):poly(styrenesulfonate) that was spincoated on the ITO coated glass to form SiNW/organic heterojunction. The results show that group BE has reflectance lower than that in group DE in solar spectrum. However, group BE has smaller power conversion efficiency (PCE) of 8.65% and short-circuit current density (Jsc) of 24.94 mA/cm2 than group DE of PCE of 9.47% and Jsc of 26.81 mA/cm2.