With the overall efficiency of the national innovation system being elevated and becoming a national strategy, as the core element supporting the national innovation system, whether top-notch innovative talents possess innovative thinking directly affects whether the national innovation strategy can be smoothly realized. However, in the current practice of cultivating top-notch innovative talents in universities, there are still problems such as emphasizing intelligence but neglecting innovation, and emphasizing external motivation-driven factors while weakening internal motivation-driven factors. Based on this, this article uses the self-determination theory as a support to explore the main components of the innovative mindset of top-notch innovative talents and the positive synergy mechanism of cultivating internal and external motivations. Therefore, this article proposes that the innovative mindset of top-notch innovative talents is an organic whole coupled by three elements: an innovative-oriented knowledge structure, thinking mode, and personality traits. The cultivation of the innovative mindset of top-notch innovative talents should focus on leveraging the synergistic effect of internal and external motivations. Firstly, universities should focus on stimulating students’ stable interest in the activities of mindset cultivation, forming the internal driving force for the cultivation of the innovative mindset of top-notch innovative talents. Secondly, universities should focus on creating an innovative cultural ecosystem, a relaxed training environment, and a diversified evaluation mechanism, forming the external driving force for the cultivation of the innovative mindset of top-notch innovative talents. Finally, universities should focus on cultivating students’ diverse knowledge systems, including disciplines, interdisciplinary, and innovative skills, and pay attention to cultivating both left-brain and right-brain thinking, allowing students to participate in innovative practices, academic research, and other activities, which not only stimulates students’ interest but also enhances their innovative awareness and ability, ultimately forming the collaborative action of cultivating the innovative mindset of top-notch innovative talents.