In order to effectively reuse the design knowledge of product family life cycle development and support holistic and rapid individual product design, this article presents a new meta-model-based systemic customization design method for complex product systems within a product-pedigree. The proposed method aims to synthetically analyze the common and adaptive customer demands and product features of a product-pedigree of complex product systems and to quickly respond to the changing demands based on knowledge accumulation in the field of customization design. The key to implement such a method is (1) to construct a product-pedigree-oriented product meta-model with a four-layered architecture where it is possible to achieve a high degree of abstraction of product and (2) to develop a special technique for configuring the meta-model of the complex product systems. We have tested the proposed method with the rapid design of product-pedigree of a high-speed train’s bogies as an illustrative example. In this work, a rapid customization design prototype system has been developed and applied to the design of a high-speed train’s bogie to illustrate how to construct a product meta-model and how to conduct configuration design on different layers and variant design for generating new products.