An iridium-catalyzed ligand-controlled semi-reduction of alkynes employing H2O as the hydrogen donor, together with its application, is reported. The use of di-tert-butylphosphinous chloride is crucial for stereoselectivity toward Z-olefins, whereas the use of 2-(diphenylphosphino)benzaldehyde is crucial for stereoselectivity toward E-olefins. More than 35 alkenes were obtained in good yields and high stereoselectivities. The utility of the current method in practical applications was investigated by studying the drug effects of (E)-1,3-dimethoxy-5-styrylbenzene on nerve growth in a zebrafish model.