For modern large-scale networked systems, ranging from cloud to edge computing systems, the topology design has a significant impact on the system performance in terms of scalability, cost, latency, throughput, and fault-tolerance. These performance metrics may conflict with each other and design criteria often vary across different networks. To date, there has been little theoretic foundation on topology designs from a prescriptive perspective, indicating that the current status quo of the design process is more of an art than a science. In this paper, we advocate a novel unified framework to describe, generate, and analyze topology design in a systematic fashion. By reverse-engineering existing topology designs and developing a fine-grained decomposition method for topology design, we propose a general procedure that serves as a common language to describe topology design. By proposing general criteria for the procedure, we devise a top-down approach to generate topology models, based on which we can systematically construct and analyze new topologies. To validate our approach, we leverage concrete tools based on combinatorial design theory and propose a novel layered topology model. With quantitative performance analysis, we reveal the trade-offs among performance metrics and generate new topologies with various advantages for different large-scale networks.