Abstract:the regional science and technology innovation resources optimization configuration is reform important embodiment in the field of science and technology, the supply side is the connotative premise of enhancing regional competitiveness through science and technology innovation. Main body participation mechanism and resources allocation mechanism are the most important parts of regional scientific and technological innovation resources allocation system, which improved ant colony algorithm is an effective method to optimize configuration of the system. According to the classification of the elements of regional scientific and technological innovation resources configured screening, due to the resource selection is a nonlinear combinatorial optimization of the process, therefore the improved ant colony algorithm through the multiple iterative operation, found that the heuristic information, the positive feedback mechanism, the pheromone volatilization mechanism are elements influence the main body participation mechanism and resource configuration of three decision factors. According to the empirical, for example, the participation of the government proposed to search for the optimal economic and social benefits under the guide of regional scientific and technological innovation resources optimal allocation system.