Mechanical training is an operation where a sample is cyclically stretched in a solvent. It is accepted as an effective strategy to strengthen and stiffen the highly hydrated silk materials (HHSMs). However, the detailed reinforcement mechanism of the process still remains to be understood. Herein, this process is studied by the integration of experimental characterization and theoretical analysis. The results from time-resolved Fourier transform infrared spectroscopy and real-time birefringent characterization reveal that the silk proteins rapidly formed a molecular cross-linking network (MCN) during the mechanical training. The cross-links were the beta-sheet nanocrystals generated from the conformation transition of silk proteins. With the progress in mechanical training, these MCNs gradually remodeled to a highly oriented molecular network structure. The final structure of the silk proteins in HHSMs is highly similar to the structural organization of silk proteins in the natural animal silk The training process significantly improved the mechanical strength and modulus of the material. With regards to the dynamic behavior of conformation transition and MCN orientation, the structural evaluation of silk proteins during mechanical training was divided into three distinct stages, namely, the MCN-forming stage, MCN-orienting stage, and oriented-MCN stage. Such division is in complete agreement with the three-stage viscoelastic behavior observed in the cyclic loading and unloading tests. Hence, a five-parameter viscoelastic model has been established to elucidate the structure-property relationship of these three stages. This work improves in-depth understanding of the fundamental issues related to structure-property relationships of HHSMs and thus provides inspiration and guidance in the design of soft silk functional materials.