A comfortable operating environment is important for the maintenance of operational capability. An evaluation method driven by cognitive efficiency of oceanauts was proposed to quantitatively evaluate the operation comfort of manned submersible operating system, which was based on the comfort characteristics of the display control interface, operation panel, and communication equipment in the system. The cognitive process of oceanauts was analyzed based on the practical operation, and the relationship between the cognitive performance, efficiency, and comfort of oceanauts was established. The cognitive efficiency model of oceanauts was constructed by using utility function according to the comfort experiment data of operating system. Support vector machines (SVM) were adopted to comprehensively investigate the influence of sub-system attributes, cognitive efficiency, age, educational background, and other factors of oceanauts on sub-system comfort perception. Through the expert weight survey method, the sub-system comfort coupling was realized and the operating system comfort was determined. Results show that the operating system could maintain a higher comfort level under the conditions that the brightness, contrast, and natural saturation of the display control interface were within [-5,0], [-50,-25], and [-5,0], respectively, the operation panel design had reasonable layout parameters and centroid position, the environmental noise frequency was low, and the communication voice sampling frequency was 48 000 Hz in communication equipment. The study indicates that the cognitive efficiency and subjective comfort have the same variation trend, and it is feasible to judge the comfort of the cabin operating system based on the cognitive efficiency of the submarine oceanauts.