In this report, alkylcarboxyl group-decorated carbon nanotubes (CNTs) with clustered functionalization patterns are achieved based on a modified Birch reduction in liquid ammonia. By using these functional CNTs (f-CNTs), a new type of Co₃O₄–CNT heterostructure is prepared via a simple hydrothermal method. SEM and TEM analyses reveal that the as-synthesized Co₃O₄–CNT heterostructures exhibit bead-on-string architecture, in which the Co₃O₄ spheres are threaded with CNTs. A possible growth mechanism is proposed to explain the formation of these Co₃O₄–CNT heterostructures. The electrochemical properties of the Co₃O₄–CNT heterostructures as anode materials for lithium ion batteries are investigated. The Co₃O₄–CNT heterostructures display high electrochemical activity, good cycle stability and improved rate performance. Such a large improvement of the electrochemical performance can be related to the robust necklace-like architectures which possess properties such as high mechanical stability, excellent electric conductivity and good strain accommodation.