The invention provides a seismic behavior based optimization method and system for a building structure. The seismic behavior based optimization method comprises the following step: A1, determining the integral target seismic behavior index of the structure and the seismic behavior index of a target construction member; A2, designing an initial structure, and dividing the construction members with the same boundary condition, the same cross section size and the same material parameter in the same layer of the structure into one class; A3, obtaining the integral damage index of the structure; A4, detecting whether the integral damage index satisfies a constraint condition, if so, performing step A5, and if not performing step 2; A5, obtaining the seismic behavior index of various classes of construction members of the structure; A6, detecting whether the seismic behavior index of various classes of construction members of the structure satisfies a condition of convergence, if so, finishing the optimization, and if not, performing step A7; and A7, determining the step size of next optimization step, updating a structural system, and returning step A3.