Cognitive ability refers to the ability to receive, process, store, and extract information. It is the most important psychological condition for people to successfully complete activities. Previous studies have shown that the design of the human-computer interface of the command and control system cannot exceed the cognitive ability of the operator of the command and control system, and it must match the cognitive ability of the operator in order to reduce the mental load intensity, and improve the accuracy, timeliness and work efficiency. However, previous researchers in the field of cognitive science have not put forward a core index system that can represent the cognitive ability of ship command and control system operators and the importance of each index, and there are few achievements that can be used for reference. To explore the core index system of cognitive ability that affecting the cognitive process of command and control system operators, and to verify the index system. Based on the classic O*NET questionnaire, two indexes of O*NET were revised, three indexes of response ability were added, and then a questionnaire on the importance evaluation of cognitive abilities index was formed. The questionnaire includes 24 indexes in six aspects: verbal abilities, idea generation and reasoning abilities, quantitative abilities, visual perception abilities, mnemonic and attentive abilities, and response abilities. The cognitive ability importance evaluation data of 202 people from different positions in the ship command and control system were collected. These data reflect the overall level of cognitive ability of operators in the whole ship command and control field. The data analysis results show that: firstly, the most important cognitive abilities affecting command and control system operators were visual perception abilities, mnemonic and attentive abilities, and response abilities. Secondly, the results of confirmatory factor analysis show that CMIN/DF, GFI, CFI, TLI, RMSEA, RMR and other indicators used in the model test all meet the requirements. The model has a good fitting degree, and the overall index extraction method is feasible. Thirdly, the independence T test results show that for beginners and experienced experts, there is a significant difference in the important evaluation of mnemonic and attentive abilities, while there is no significant difference in the important evaluation of response and visual perception abilities. Fourthly, the results of Bi-group confirmatory factor analysis experiment show that the structural model has good stability and factor invariance. Through the research of this paper, the index system which can express the core cognitive ability of the commander of command and control system is successfully constructed, and the index system has been fully verified by mathematics. The 3 abilities and 10 indexes in the index system are closely related to the work tasks of operators, which also reflects the correctness of our construction results to a certain extent. According to the results of data analysis, there are differences between assistant commanders and professional commanders in the evaluation of the importance of some indexes, which reflects the importance of working age and experience to the promotion of position skills. The results of this research are of great significance for the subsequent acquisition of cognitive ability data and assessment of post cognitive ability of command and control system operators.