Multifunctionality is one of essential elements which enables nanomaterials to be used in the field of nanobiomedical applications. Since simple integration of differently functioning nanoparticles (NPs) in a confined space could lead to malfunction or interference between the NPs, a method that can spatially isolate the NPs and can be applied to a wide range of NPs is highly required. In this work, we developed an efficient method that can be used to stack SNTs with various NPs for the preparation of multifunctional nanotube, which is involved with hydrophobic interaction between NPs and the inside of SNTs. In addition, we successfully demonstrated that barcode nanotube coded by different colored quantum dots and multifunctional SNT with magnetic, fluorescent, and potent SERS‐active properties can be fabricated using the stacking method.