Hydrogels are 3D cross-linked polymer networks. Benefiting from the flexible designs and reasonable constructions of these networks, a large number of smart hydrogels with response characteristics to specific stimuli have received widespread attention and developed rapidly. The skeletal networks composed of the skeletal polymer chains and effectual cross-links are the soul of such soft materials, and the response behaviors fundamentally depend on the dynamic characteristics of skeletal networks. Herein, the novel concepts of skeletal networks analysis to describe, understand, and guide the advanced designs and applications of smart hydrogels are proposed. Representative glucose-sensitive hydrogels and DNA-based smart hydrogels are reviewed to demonstrate the principle of skeletal networks analysis and clarify its practical guidance. Summarizing and classifying the characterizations and conversions of skeletal networks dynamics based on different response mechanisms provides a realistic solution. On this basis, advanced applications of smart hydrogels guided by skeletal networks dynamics including biochemical detection, cell mechanics sensing, drug delivery systems, and dynamic complex soft materials are typically reviewed. The skeletal networks analysis for smart hydrogels is of great significance for understanding the microstructures of hydrogels and guiding the designs of soft materials and their smart applications in the fields of analytical science and advanced materials.