Surface-enhanced Raman scattering (SERS) has been widely reported to improve the sensitivity of Raman spectra. Ordinarily, the laser is focused on the sample to measure the Raman spectrum. The size of the focused light spot is comparable with that of micro-nano structures, and the number of micro-nano structures contained in the light spot area (defined as duty cycle) will severely affect the spectrum intensity. In this study, flower-like silver nanostructures were fabricated with a soft lyotropic liquid crystal template in order to investigate the effect of duty cycle. They were observed under a scanning electron microscope, and their spectrum enhancement factor was computed with the obtained Raman spectrum. Then, their duty cycles were measured using a SERS substrate at different locations. A formula was derived to represent the relation between the duty cycle of the nanoflowers and the Raman spectral intensity. This work could promote the actual applications of SERS in high-sensitivity spectrum testing.