In this paper, a co-optimization design method for thermal-stress coupling 3-dimensional integrated system with through silicon via is proposed based on the finite element method, support vector machine model and modified particle swarm optimization algorithm. In the cause of analyzing the effects of geometrical parameters (radius of through silicon via, oxide thickness and the height of oxide insolation layer) on the thermal-stress distribution, the finite element method based COMSOL software is conducted to simulate the thermal-stress coupling 3-dimensional integrated system. Based on the simulation data obtained by COMSOL, the support vector machine models are adopted to establish the database for describing the relationships between the geometrical parameters and key indexes (peak temperature, peak stress and temperature difference) to improve the design efficiency. Based on the desired key indexes of thermal-stress coupling 3-dimensional integrated system, the multi-objective evaluation function is formulated. Then, the geometrical parameters are optimized by the modified particle swarm optimization algorithm. The finite element simulation is conducted to verify the effectiveness of the proposed strategy. In three cases, the errors between the simulated and desired temperature differences are all less than 0.28 K, and the relative errors between the simulated and desired peak temperature/peak stress are all less than 4.78%, which indicates that the geometrical parameters can be optimized to control the key indexes of thermal-stress coupling 3-dimensional integrated system. Therefore, the developed method can be used in the design and manufacture of 3-dimensional integrated system.