This paper proposes a new system design methodology called the Cost-Specification Analysis. The method seeks to satisfy both target cost and required functionality simultaneously. The method assumes that the worth of a product’s structure such as a main system, a sub-system, an assembly and a part, or its specifications is proportional to its degree of contribution to fulfill the customer needs. The paper first presents systematic procedure to allocate the importance of the “Voice of the Customer” to product’s structures and their specifications. The Cost-Specification Analysis evaluates design concept candidates based on the target cost of a structure calculated from its worth, and the target specifications. The design concept that satisfies both the target cost and the specifications should lead to larger customer satisfaction and financially successful product. The design concept selection of a particle beam control system in linear accelerator serves as an illustrative example.