Halloysite nanotubes (HNTs) are natural occurring mineral clay nanotubes that have excellent application potential in different fields. However, HNTs are heterogeneous in size, surface charge, and formation of surfacial hydrogen bond, which lead to weak affinity and aggregation at a certain extent. It is very important to modify the HNTs’ surface to expand its applications. In this review, the structural characteristics, performance, and the related applications of surface-modified HNTs are reviewed. We focus on the surface-modified variation of HNTs, the effects of surface modification on the materials and related applications in various regions. In addition, future prospects and the meaning of surface modification were also discussed in HNTs studies. This review provides a reference for the application of HNTs modifications in the field of new nanomaterials.