This paper presents an integrated hyper specification documentation (IHSD) methodology and tool for coherent software engineering documentation. The IHSD tool is designed for automatically creating hyperlinks between system conceptual models in UML; formal models in real-time process algebra (RTPA); and code in a programming language. The three types of design documents for a system in UML, RTPA, and C++ program are stored in a standard HTML file format. When a built-in hyperlink in a system model is clicked, the corresponding HTML page in the integrated file is show up. The IHSD method provides a powerful and convenient integration of traditionally separated system design documents by hyperlinks in a coherent environment. Under the support of the IHSD tool, readers can traverse from any point of interested objects to any other ones among the conceptual and formal models of systems as well as corresponding programs. Therefore, the readability and maintainability of large-scale software systems are dramatically improved