The main work pattern of harbor engineering investigation and design industries is two dimensional separated working. Its features are designed separatedly. The data store in different documents and tables, and information exchange by lettering. This pattern is not only ineffective and difficult to share data, but also makes mistakes and omissions easily. This article proposes a new work pattern of harbor engineering investigation and design industries, which is three dimensional designing based and with whole production process integrated, realizes full profession three dimensional design, seamless data link, customizable auto analysis, customizable result data output and product lifecycle management. This article proposes the system design of the new pattern. The design divides the system into three levels, taking account of generality and specificity of engineering design and realizing good system architecture separation and well system expandability.