The cross section of circular cylinder in their dynamic model is always considered as a perfect circle, which means radii at every point on the circle are the same. In real engineering structure, there are slight fluctuations in shape of the circular cylinder which is different from those in ideal model. Meanwhile, effects of structural fluctuations on its dynamic characteristic are rarely analyzed before. To study problem mentioned above, the geometric shape of a typical, apparently symmetrical cylinder is examined experimentally to demonstrate that a small variation in diameter and thickness indeed exists in practice firstly. Because fluctuations in diameter and thickness of the cylinder are related to each other, we need to separate effects of a slight variation in its diameter and thickness on structural dynamic characteristics to search the key factor of influence. Then, two simplified modes, which are modeled by finite element method, are used to study the effects of diameter or thickness variation alone on the natural frequencies and modal shapes of the free cylinder. It is revealed that the diameter variation described by the simplified model captures the key influencing elements which affect the modal characteristics of the free cylinder. Finally, a free cylinder with both variations is analyzed numerically and the results are verified experimentally. This work illustrates that significant discrepancies inevitably exist between the measured results of an actual free cylinder and an assumed symmetrical model even if there is only a very slight variation in its geometric shape.