Nanomotors are usually designed to work in liquid media and carry cargo; they exhibit excellent potential for biosensing and disease treatment applications due to their small size. Graphene and carbon nanotubes (CNTs) are crucial components of rotary nanomotors because of excellent mechanical properties and adaptability to the human body. Herein, we introduce a DNA−CNT-based nanomotor that achieves its rotational control through an array of nanopores with tunable surface charges. The findings demonstrate that by adjusting the surface charge density of the nanopores and the direction of electric field, a DNA strand can be sequentially captured by the nanopores, thereby rotating the connected CNT. The transition from a four-nanopore array to a six-nanopore array reveals that reducing the step angle to 60°significantly enhances the rotational stability of the nanomotor and reduces random fluctuations caused by Brownian motion. This method improves the control stability of the nanomotor, providing robust support for future applications in nanoscale manipulation.