Serious games combine pedagogy and interactive learning to foster high intrinsic motivation and positive player experience; they can increase participant interest and make the training process more enjoyable, memorable and effective. The multi-layer model provides an approach to analyse and evaluate serious games design in a collaborative (designer, professional and player) and iterative process. In this paper, we propose a multi-layer methodology of serious games based on the design, play and experience framework (DPE) often used in instructional design, this methodology will help game designers, especially the beginners to analyses their own serious games easily, and will allow professionals to evaluate and provide a guideline of design in collaboration with several actors.