Aiming at eccentricity in the central position at the top of variable section pier during construction and based on the current stability theory, this paper studies the stability calculation of variable section slender pier with initial eccentricity in order to evaluate the availability of the pier. Firstly, theoretical equations to calculate the critical load of variable section compressed bar under ideal condition are derived in accordance with the functional principle. And the corresponding critical loads are worked out through using these formulae. Then, Finite Element Method (FEM) ANSYS is adopted to establish the spatial solid models of the bridge pier with or without initial eccentricity respectively. Critical load values of variable section slender pier under ideal condition are figured out, which are compared with the theoretical values in order to check the model’s reliability. On these bases, researches on stability of pier are performed and stability of the pier with initial eccentricity is calculated under the worst load condition at the stage of construction and completed state. Finally, all the calculated results are compared with Code’s specified values to judge the availability of this pier, which provides a firm protection for project constructions.