This chapter employs a cross-theory perspective by combining the four theories of agency theory, resource-dependent theory, resource-based theory, and knowledge- based theory, intending to explore the impact of inter-organizational strategic alliance on organizational value-based decision-making model and intellectual capital. Drawing the related variables upon making the literature review, analysis and inference, it infers 18 propositions and builds up a conceptual model. As a result, it is found that different formation factors of inter-organizational strategic alliance not only have significanty impact on an agency problem, but also have positive or negative impact on core resource and core knowledge strategic alliance. It is also found that when there is an inter-organizational agency problem, it will further increase the agency cost, and impact on the organizational value-based decision of inter-organizational strategic alliance in the future. Furthermore, the authors hope that researchers understanding through the governance mechanisms of inter-organizational core resource alliance and core knowledge strategic alliance are more matured, it will be more effective to prevent the appearance of agency problem and reduce agency cost and will be more helpful to the increase of organizational intellectual capital and the creation of organizational value.