Based on the command relationship in unified air defense, firstly, three typical command organization structures are built. From the point of view in command information transmission, according to the selecting principle of evaluation index, and in combination with the factors influencing the command organization structure rationality in unified air defense, an index system of the command organization structure rationality is put forward, and a measure model of index is also established. Secondly, with the application of grey clustering theory, the evaluation method of unified air defense rationality is discussed, and the calculating steps are presented. Finally, an analysis of the examples of the three typical command organization structures is given, and the result shows that this method is simple and feasible.