Knot tying is a critical task in robotic surgery, which is considerably important for surgical success and postoperative recovery. Despite of the well-established protocols and significant progress using medical robots at macro scale, the need for automatedly tying mechanically robust knots on mini-incisions remains largely unmet, particularly with relieved suture deformation, avoided suture slippage, reduced workspace consumption, and enhanced precision and biomechanical compatibility. Here, we propose an innovative dual-arm nanorobotic system featured by stereo microscope and additional rotation degree of freedom (DOF) mounted on each arm, enabling automated, precise, and controllable knot tying on mini-incisions. With this system, a synchronous rotation-based knot tying (SRKT) trajectory is designed to mitigate undesired suture deformation, suture slippage, and minimize workspace consumption. The theoretical and simulation analysis of the topology and tension force distribution on suture validated the efficacy of SRKT trajectory. The experiments demonstrated that the dual-arm nanorobotic system with SRKT trajectory can be used for tying various knot types, using different micro-sutures, conducting on mini-incisions of different tissues, especially keeping suture slippage avoidance, minimal workspace, and robust mechanical strength of the tied knots. The proposed dual-arm nanorobotic system and SRKT trajectory render a significant potential for various practical medical applications.