This paper analyses the cognitive aspect of intelligent design and points out that the nested structure of a human being’s cognition on a complex design object, which is generated by thinking iteration while design thinking being in the chaotic state is the fundamental mechanism of intelligent design. A taxonomy of design problems is given based upon fractal theory and a complex design problem is considered as a fractal in our approach. Some new concepts such as granularity, refinement and coarsening are defined. Based upon the concepts of a cluster of problems and designs, the nested design, a new model for intelligent design, is proposed as continuity of the above work. The main steps of the nested design are listed and an illustrated example is given to demonstrate its implementation. The characteristics of the nested design show that it is the design methodology oriented to complex design problems.