A more applicable optimization model for extracting flutter derivatives of bridge decks is presented, which is suitable for time-varying weights for fitting errors and different lengths of vertical bending and torsional free vibration data. A stochastic search technique for searching the optimal solution of optimization problem is developed, which is more convenient in understanding and programming than the alternate iteration technique, and testified to be a valid and efficient method using two numerical examples. On the basis of the section model test of Sutong Bridge deck, the flutter derivatives are extracted by the stochastic search technique, and compared with the identification results using the modified least-square method. The Empirical Mode Decomposition method is employed to eliminate noise, trends and zero excursion of the collected free vibration data of vertical bending and torsional motion, by which the identification precision of flutter derivatives is improved.