The design and analysis of the secondary air system (SAS) of gas turbine engine is a complex and time-consuming process because of the complicated topology and iterative nature of SAS design. The conventional SAS design-analysis model generation process is quite tedious and inefficient. It is still largely dependent on human expertise and thus incurs high time-cost. This paper presents an automated, whole-engine SAS flow network model generation methodology. This method accesses a prebuilt feature-based whole-engine geometry model and transforms the geometry features into the features suitable for SAS flow network analysis. The proposed method extracts both the geometric and non-geometric information from the engine geometry model such as rotational frames, materials, and boundary conditions. Apart from ensuring geometric consistency, this methodology also establishes a bidirectional information exchange protocol between the engine geometry model and the SAS flow network model, which enables to make engine geometry modifications based on SAS analysis results. The application of this feature mapping methodology is demonstrated by generating the SAS flow network model of a modern three-shaft gas turbine engine. This flow network model is generated within a few minutes, without any human intervention, which significantly reduces the SAS design-analysis time cost. The proposed methodology seamlessly links the geometry and the air system modelers of Virtual Gas Turbines simulation framework and thus allows performing a large number of whole-engine SAS simulations, design optimizations and fast redesign activities.