The measurement of trajectory distance is the base of trajectory clustering. To deal with the flight trajectory clustering in air traffic, a novel method is proposed in this paper to measure the flight trajectory distance. This method views the trajectory as a set of segments, whose end points are trajectory points, and it measures the distance from a trajectory point to another trajectory, and thus presents the distance definition of trajectories. Based on the calculated distance matrix, spectral clustering algorithm is adopted to cluster flight trajectories. The experiment on actual flight trajectory data verifies the effectiveness of the proposed method.