This paper discusses whether the ergonomic assessment of the man-machine interface of the ship console in virtual reality simulation system can achieve the effect similar to that in physical simulation system. The similarity of the two systems was verified by assessing the situation awareness level of the subjects. 9 subjects were recruited to participate in the comparative experiment of ship navigation tasks in two systems, which 13 tasks were designed under the three conditions. 10D-SART scale, situation awareness global assess technique (SAGAT), eye movement data and performance were used to assess the situation awareness of subjects. The results provided there is a high consistency and no significant difference among the indices between the virtual reality simulation system and the physical simulation system. Among these indices, the response or operation time and gaze entropy had the highest correlation between the two systems, and the correlation of condition 2 and condition 3 were all above 0.9. SART score and SAGAT score had the second highest correlation between the two systems, and the correlation in each working condition reached about 0.7. Under the influence of different conditions and different users, SART scores and SAGAT scores of the three conditions had no obvious change trend. The results show that the virtual reality simulation system can replace the physical simulation system to a certain extent in the assessment of the operator’s situation awareness. This method can be used for the scheme assessment in early stages of design to reduce the development costs greatly.