A two-stage damage identification method for beam structures based on support vector machine and swarm intelligence optimization algorithms is proposed. First, the frequencies and mode shapes of the beam structure are obtained using the smooth orthogonal decomposition method, and the normalized modal curvature is calculated as the input of a pre-trained support vector machine to determine the damage location. Then, the stiffness loss at the damaged location of the structure is calculated using swarm intelligence algorithms. The fitness function is the sum of the residual squares of the frequencies of the damaged structure identified by the smooth orthogonal decomposition method and the frequencies calculated for each iteration of the intelligent optimization algorithm. Numerical examples of a damaged simply supported beam structure are used to verify the damage identification performance of the two-stage method. The accuracy of the support vector machine model under different damage degrees and noise levels is studied using the Monte-Carlo method, and an uncertainty of the damage degree prediction value is studied by comparing the particle swarm optimization algorithm, moth-fire algorithm, and mayfly algorithm.