Abstract:At present, the significance of large scale scientific facilities becomes more apparent to the national scientific and economic construction, which puts forward higher requirements for the operation evaluation of the facilities. However, the present and commonly used operation evaluation index system has certain deficiencies in terms of logicality, suitability and comprehensiveness. Therefore, this article introduces the soft system method to construct the evaluation index system for the operation of large scale scientific facilities. Guided by the opinions of the relevant parties of the facilities, the research realizes the comprehensive consideration of the whole process of "input-transformation-output" of the facilities, and conducts an empirical study by taking the synchrotron radiation source as an example. The results show that the evaluation index system constructed based on this method can clarify the logical relationship between the indexes, is more systematic and flexible, and has great significance in the operation planning of large scale scientific facilities.