Ship engine room system design is a key part of ship design. Just like the ship design, computer aided ship engine room system design started at quite early time. However, despite the geometric layout, the calculation of ventilation capacity is related to whole design. In this paper, we successfully integrated both computer works into a working system. In addition, two unique concepts are proposed to improve the ventilation system design. First is the utilization of reference drawings of ship structure and equipments. Second is the using of primary and secondary pipe generation, editing and auto-renumbering techniques. A flow chart is presented to show this improved working procedures, and a 3D sample system is illustrated.