Surface-enhanced Raman resonant scattering (SERRS) tags encoded with near-infrared (NIR) Raman reporters showed great potential for in vivo detection owing to their ultrasensitivity. However, in vivo signal stability of such tags is a remaining problem due to the lack of suitable silica coating method because the weakly adsorbed NIR reporters tend to detach from traditional gold nanosubstrates in the ethanol-rich and high pH conditions, which are commonly used for silica coating. Herein, we propose a silica coating method for NIR SERRS tags by using waxberry-like gold nanoparticles (NPs) as substrates. The lipid bilayer of the NPs played a crucial role in the coating, which can encapsulate the NIR Raman reporter via hydrophobic interactions and prevent the interference from a harsh medium. Thus, the silica-coated tags well preserved ultrasensitivity of bare tags and simultaneously gained satisfactory signal stability in vivo. Moreover, the coating method is compatible for the encapsulation of a variety of thiol group-free NIR reporters (as exemplified by DTTC, Cy7, IR792, and DIR), relying on which a tag-pair with distinguishable peaks can be screened (labeling with DTTC and Cy7, respectively). In vivo duplexing detection revealed that the tag-pair-labeled liposome was cleared faster in the liver than polydopamine NPs within one mouse. The developed method paves an easy way for gaining high-quality SERRS tags and will promote their in vivo multiplex analysis and diagnostics applications.