In the traditional Confucian gentleman culture, Chinese entrepreneurs have cultivated unique mindset and have harnessed such mindset in managing the government-business relationship, which is strategically critical for innovation. This paper builds a theoretical framework of Confucianist entrepreneurship—collaborative innovation—enterprise performance, studies the impact of such entrepreneurship on enterprise performance. From the perspective of collaborative innovation, internal innovation mechanism has been studied, and the moderating effect and conditional boundary of the cordial and clean government business relationship have been further validated. A survey of 1,437 micro, small and medium-sized enterprises (MSMEs) made in China in 2019 found that: (1) Confucianist entrepreneurship has a significant positive impact on promoting the enterprise performance; (2) collaborative innovation has demonstrated the action mechanism of Confucianist entrepreneurship on enterprise performance; (3) the cordial and clean government-business relationship positively moderates entrepreneurship on enterprise performance. It also has the positive intermediary effect on collaborative innovation between Confucianist entrepreneurs and enterprise performance. This study has not only expanded the scope of research on entrepreneurship and Confucian culture and ethics, but has also extended the integration of entrepreneurship and collaborative innovation to the micro level, providing theoretical and practical inspiration for the innovation practices of small and micro-sized (SMEs) enterprises.