As the complexity of system rising day by day, the idea of system engineering is used in civil aircraft design more and more, and the model based system engineering (MBSE) is the trend. This article described the concept and process of civil aircraft design based on MBSE method and three important standards which bring a lot of benefit to MBSE during its development. Then it listed a few familiar software tools which are wildly used in deferent stages of MBSE process. And it also proposed the tool chain architecture of MBSE which can provide a good reference for making MBSE practicable in civil aircraft design.