Based on the surface-enhanced Raman scattering enhancement effect of SiC@Ag substrate and Ag nanoparticles, an ultrasensitive miRNA-106a detection protocol was proposed by using the second surface-enhanced Raman scattering amplification of the silver-biotin-streptavidin nanoaggregates. First, SiC@Ag@anti-digoxin/digoxin-DNA substrate was prepared by specifically binding of a capture DNA modified with a digoxigen group and an anti-digoxin immobilized on a SiC@Ag substrate. The Ag@4MBA@DNA-biotin probe was prepared by linking the amino/biotin-modified probe DNA with the 4-mercaptobenzoic acid (4MBA) immobilized silver nanoparticles. Then, the "sandwich" structure was constructed by Ag@4MBA@DNA-biotin probe, target miRNA-106a and SiC@Ag@anti-digoxin/digoxin-DNA substrate to amplify the surface-enhanced Raman scattering signal. Finally, the streptavidin and the extra probes were alternately added into the “sandwich structure” to form the silver-biotin-streptavidin nanoaggregates and achieve secondary amplification of the detection signal. The experimental results show that the ultrasensitive detection of miRNA-106a has been implemented by using the dual surface-enhanced Raman scattering amplifications of SiC@Ag substrate and silver-biotin-streptavidin nanoaggregates, arriving an ultralow detection limit of 0.579 fmol/L, which has a potential for early diagnosis of tumors.