Government of Taiwan has aimed to establish a simplified and flexible government organization long time ago. In addition to promote the legislation of organization reform continuously, the presence of an effective organization assessment mechanism is also indispensable. As the assessed party may anticipate changes in the result of the organization assessment, organization assessment may be easily interfered by abstract factors such as organization inertia, politics, organizational behavior and more, thus affecting the results of the assessment and the decisions made. This article attempts to discuss latent influences that are easily neglected in the assessment process and serves as a reference for the establishment of the government organization assessment mechanism.