We demonstrate the selective adsorption of Ni/Si shell/core nanowires (Ni-Si NWs) with a Ni outer shell and a Si inner core on molecularly patterned substrates and their application to sensors for the detection of chlorine gas, a toxic halogen gas. The molecularly patterned substrates consisted of polar SiO2 regions and nonpolar regions of self-assembled monolayers of octadecyltrichlorosilane (OTS). The NWs showed selective adsorption on the polar SiO2 regions, avoiding assembly on the nonpolar OTS regions. Utilizing these assembled Ni-Si NWs, we demonstrate a sensor for the detection of chlorine gas. The utilization of Ni-Si NWs resulted in a much larger sensor response of approximately 23% to 5 ppm of chlorine gas compared to bare Ni NWs, due to the increased surface-to-volume ratio of the Ni-Si shell/core structure. We expect that our sensor will be utilized in the future for the real-time detection of halogen gases including chlorine with high sensitivity and fast response.Electronic supplementary materialThe online version of this article (doi:10.1186/s11671-015-0729-2) contains supplementary material, which is available to authorized users.