Halloysite nanotubes (HNTs) have emerged as one of the promising clay minerals that have myriad applications due to their unique properties. The presence of silica and alumina groups on the outer and inner surfaces allows surface modifications with different functional compounds. Depending on the applications required, numerous desired compounds have been used for both inner and outer surface modifications to construct hybrid noanostructures which further enhance their physiochemical properties. This review discusses the surface design with special emphasis on magnetic nanoparticles to fabricate HNT-based magnetic nanostructures which display synergistic effects and summarizes potential applications in the fields of catalysis, magnetically driven drug delivery, chemotherapy/diagnosis, environmental remediation, emulsification, and microwave absorption.