Surface acoustic wave (SAW) gas sensors with nanostructured material-based sensing layers are desirable in gas sensing owing to their high sensitivity, and their fast response and recovery time. In this work, a novel SAW gas sensor with a nanostructured silicon (Si)-based sensing layer with four pairs of aluminum-based input and output interdigital transducer (IDT) is developed and fabricated. A finite-element analysis (FEA) is used to determine the sensitivity while varying the height of the nanostructured Si. As a proof of concept, the SAW sensor is tested for carbon dioxide (CO2) gas concentrations, ranging from 500 to 2000 ppm. The results demonstrate that the developed SAW sensor with a nanostructured Si-based sensing layer showed a maximum frequency shift of 4.62177 kHz with a response and a recovery time of 31 and 40.5 s, respectively, for a 2000-ppm CO2 gas concentration. The developed nanostructured Si as a sensing layer for the SAW gas sensor demonstrated higher sensitivity than previously reported devices and has promising potential to be used as a sensing layer for next-generation MEMS SAW gas sensors.