In this article, we report an ultra-thin shell of MoS2 (3–7 nm) deposited on Ag nanowires (AgNWs) to form a core-shell hybrid system by the sol-gol method. Since AgNWs is easy to be oxidized, a protection shell is necessary. Compared with commonly used hydrothermal method for MoS2, it could produce a more thinner and homogeneous shell with the least 3 nm thickness of MoS2 shell, which is a breaking-through of making MoS2 shell based on noble nanoparticles. Results show that the obtained hybrid system has great value on surface-enhanced Raman spectroscopy (SERS) due to surface plasmon resonance (SPR) effect of Ag nanowires. Ultra-thin MoS2 shell was suitable for protecting AgNWs and simultaneously had excellent SERS signature, and this effect was rare for MoS2 shells. By decreasing the thickness of MoS2 film from 7 to 3 nm, the intensity of SERS signal could be enhanced. It was observed that the microstructure of this AgNWs@MoS2 system consist of crystal AgNWs surrounded by crystal MoS2. AgNWs@MoS2 showed excellent SERS effect with Rhodamine 6G (R6G) and N719 dyes, the detection limit could reach to 10−5 M. Finally for comparison, local electromagnetic field enhancement of AgNWs@SiO2 was also simulated to indicate AgNWs@MoS2 better.