Abstract
Engineering research center is the important composition part of national innovation foundation construction. It is a new economic entity which is developing and improving at present. The paper analyses the existing problems which engineering research center adopts the traditional functional organizational structure, proposes that engineering research center is suitable to take matrix organizational structure based on the thinking of project management according to its own characteristics, use the theory of structure entropy to evaluate the order degree of the two organizational structures of engineering research center. The result reflects that the order degree which engineering research center adopts matrix organizational structure is better than the one of functional organizational structure, which realizes the organizational structure optimization of engineering research center.
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