This study reported the significantly improved Raman enhancement ability of silver nanoparticles (Ag NPs) by decorating them on single NaYF4:Yb,Er@SiO2 core-shell particles (UC@SiO2@Ag) under a 785 nm excitation. The optimal thickness of the silica shell can be easily obtained by adjusting the amounts of TEOS, which is the crucial element to balance the upconversion and the formation of a hot spot by Ag NP aggregation. This substrate revealed highly reproducible properties, which is crucial to the practical application of SERS technology. This substrate exhibited an excellent sensitivity for methylamphetamine detection under near-infrared excitation. The advantages of NIR excitation in our SERS sensing open up a new application field of UC-noble metal composites, and also promise a new research direction for the synthesis and applications of SERS-active nanostructures.