The rise of the cross-boundary alliance as a new organizational model profoundly affects innovation development. The incentive mode of knowledge-sharing among cross-boundary alliance members from the perspective of symbiosis is the key to improving the efficiency of knowledge-sharing and promoting the alliance’s sustainable development. Due to the interdisciplinary nature of knowledge and information asymmetry among alliance members, knowledge-sharing is prone to opportunistic behavior, which greatly impacts cross- boundary innovation cooperation. The symbiotic system of the cross-boundary alliance is constructed based on the analysis of symbiosis among alliance members to solve these problems. In this research study, the principal–agent theory is used to describe the expected benefits and the related constraints of knowledge-sharing partners. Moreover, an incentive model of knowledge-sharing in the cross-boundary alliance is established. By solving the model, the agent’s sharing intention and the principal’s reward incentive coefficient are obtained, which provide a theoretical basis for the formulation of the optimal incentive scheme of knowledge-sharing in the alliance. The results show that the knowledge potential difference, knowledge transmission efficiency, knowledge transformation, innovation effort, and the symbiotic environment will directly affect the knowledge transfer level of the alliance. In this research study, a theoretical research framework of the cross-boundary alliance symbiotic system linked by knowledge-sharing is constructed. The incentive model of knowledge-sharing is established especially on the basis of fully considering the internal and external factors of knowledge-sharing. This research study has provided some innovation in the theoretical system and method improvement, and has guaranteed the efficient integration, utilization, and innovation of knowledge resources in the cross-boundary alliance.