A 240 m-height RC chimney was chosen as the research object. Composite shell element was adopted to establish the nonlinear analytical model by using the finite element software ABAQUS. In order to perform the incremental dynamic analysis considering the uncertainty of the ground motions，20 ground motion records were selected based on the matched-spectrum principle. The peak ground acceleration and maximum strain were selected as the intensity measure and engineering demand parameters，respectively. Based on the material strain of concrete and steel rebar，the limit values of four damage states were defined. The base excited by the ground motion has seven different angles during incremental dynamic analysis. Combining with the response of structure obtained by incremental dynamic analysis，the vulnerability was calculated by the curve fitting method. The seismic fragility and collapse probability curves of high-rise RC chimney structures under different ground motions were then obtained. The results show that when the PGA is smaller than 0.2 g，the critical input angle is approximately 75°~90° and the complete damage probability increases about 1.5% considering directionality of three-directional earthquake. When the PGA is bigger than 0.2 g，the critical input angle is 45° and the complete damage probability increases about 2.4%.