Tremendous attention has been paid to the structure and properties of silk fibroin/sodium alginate (SF/SA) composite films. However, there is no report devoted to study the formation of hydrogen bonds and their effects on the structures and properties. Herein, SF/SA blends with different mass ratios were obtained and the technic of Gaussian multi-peaks-fitting of Fourier transform infrared spectrum (FTIR) was used to analyze their hydrogen bonds. From the results, the existence of the intermolecular and intramolecular hydrogen bonds was manifested, and the relative strength of the intermolecular hydrogen bond enhanced with the increase of SA content. The contribution of the intermolecular hydrogen bonding was as follows: OH center dot center dot center dot O (ether) > OH center dot center dot center dot pi > OH center dot center dot center dot N. Meanwhile, the increase of intermolecular hydrogen bonding led to the increase of apparent viscosity of the SF/ SA blend solutions. Moreover, the relationship between the hydrogen bond and properties (e.g, crystallinity, thermal stability, mechanical properties, morphology and etc.) of SF/SA composite films with different mass ratios were analyzed in detail.