Active vibration control of large laminated cylindrical structures, for example, the cabin of space, air, surficial or subaqueous vehicles, usually requires multiple inputs and multiple outputs to the system, since there are usually multiple vibration sources and each source contains multiple frequency components. The performance of multiple inputs and multiple outputs control system will be dramatically affected by the complex dynamic behavior of the laminated cylindrical structure, thus an effective model is in great request in analyzing and designing the control system. However, there is seldom distributed parametric model, typically, finite element model, applying to the active vibration control system, because of its computational complexity. In this work, we propose an effective finite element model in-loop system of laminated cylindrical structure for multiple inputs and multiple outputs active vibration control simulation. Firstly, an finite element model of laminated thick cylindrical structure with four-node Mindlin degenerated shell element has been constructed. Then, a model reduction procedure has been proposed to obtain in-loop model of the control system. The numerical global modal analysis and harmonic response analysis of the cylindrical structure have been conducted to verify the correctness of the model. Afterward, a multiple inputs and multiple outputs adaptive algorithm which is able to coup with multiple frequencies and multiple sources vibration has been applied to the finite element model in-loop system. Finally, four numerical case studies have been conducted, in which the vibration sources contain multiple frequency components and artificial colored noises. The result shows that the vibration of the multiple control points can be dramatically suppressed simultaneously, which demonstrates the effectiveness of the algorithm and finite element model in-loop system.