The naval multi-function console provides various types of information to the operator. It is equipment that is key for submarine navigation, and fatal human errors can occur due to the mismatch between the console specifications and the operator’s body size. This study proposes a method for deriving console specifications suitable for the body size of Korean users. The seat height, seat width, seat depth, upper edge of backrest, and worktable height were selected as the target design variables. Using six anthropometric dimensions, a mismatch equation for each target design variable was developed. Anthropometric measures of 2027 Korean males were obtained, and the optimal specifications of the console were derived via an algorithmic approach. As a result, the match rate, considering all the target design variables, was improved from 2.57% to 76.96%. In previous studies and standards, the optimal console specifications were suggested based on the anthropometric data of a specific percentile of users, and it was impossible to quantitatively confirm the suitability of the console design for the target users. However, the method used in this study calculated the match rate using the mismatch equation devised for comfortable use of the console and a large amount of anthropometric data that represented the user population, and therefore the improvement effect of the recommended specification can be directly identified when compared to the current specifications. Moreover, the methodology and results of this study could be used for deciding the specifications of multi-function consoles in several fields, including nuclear power plants or disaster situation rooms.