Electro-hydraulic shaking table is an essential experimental apparatus to evaluate structural performance under actual vibration condition. The control-structure interaction (CSI) between shaking table and eccentric load has lately received considerable attention for causing the accuracy degradation of shaking table test. At present, the research gap of the influence of the eccentricity of load on the CSI makes it challenging to find the CSI effects. And an effect assessment is yet to be proposed to evaluate the CSI effects, which has impeded the development of test technology. To overcome those theoretical bottlenecks, in this research, an analytical transfer function matrix of shaking table and eccentric load is established to analyze the CSI effects. The analysis is conducted under such conditions as different mass ratio (MR), moment of inertia ratio (IR), and eccentric distance ratio (ER) conditions. Through the analysis, the role of the ER is identified, the sensitivities of the MR, IR, and ER to the transfer function matrix are revealed, and the CSI effects are found. Furthermore, a novelty effect assessment is proposed to appraise whether the CSI effects can be ignored in shaking table test. And the visualization expression of the effect assessment is obtained for convenient application.