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Nonlinear factors exist in electro-hydraulic shaking table and may distort the response signal when a sinusoidal acceleration is inputted. To obtain accurate harmonics, a harmonic identification strategy for the acceleration of the electro-hydraulic shaking table based on the SA-PSO (Simulated Annealing-Particle Swarm Optimization) algorithm was proposed. First, the criterion function of harmonic identification was built with the least square method. Then, the PSO algorithm was introduced into the internal circulations of the SA algorithm to speed up the local search speed to construct the harmonic identification strategy. To verify the performance of the identification strategy, the SA algorithm, PSO algorithm, and SA-PSO algorithm were successively used to identify the response signal. And the convergence rate, accuracy, and stability of the three algorithms were compared. Finally, the harmonic regeneration was carried out after the amplitude and phase of each harmonic were obtained. Experimental results show that the harmonic identification strategy has fast identification speed and high identification accuracy.