Regarding the impact mechanism of inter-organizational relationships on innovation activities, there are different views proposed by transaction cost theory and social capital theory. The internal complexity originating from innovation ambidexterity also leads to vague understanding of its mechanism. Not recognizing the dynamic of the organizational boundaries is an important cause for paradoxical viewpoints, which leads to more complex inter-organizational relationship and uncertain innovation activities. Transaction cost theory and social capital theory can only provide effective explanations in their independent research scopes and specific contexts, but it is difficult to systematically explore and exploit the internal mechanism of management activities. The paper distinguishes the paradoxical viewpoints of the two theories and its basic causes, and then based on the “theoretical fusion and cross-boundary fusion”, proposes that a new type of inter-organizational relationship be established through the dynamic adjustment of organizational boundaries, and a cross-boundary fusion area be formed between the relative boundary and the absolute boundary in co-innovation pattern. The fusion of transaction cost theory and social capital theory can provide new theoretical perspectives to precisely explaining the phenomenon of using economic transactions and social connections to achieve the balance and combined of innovation ambidexterity. The new research viewpoint not only resolves the paradox viewpoints in previous studies, but also enhances the interpretation of management practices.