A kind of low molecular weight of chitosan was modified to water-soluble chitosan quaternary ammonium salt (short for HTCC) in this paper, where after, the Bombyx mori silk fiber and fabric were both treated by HTCC solution. The aggregation structure of silk fiber and the antibacterial performance and dyeing behavior of silk fabric treated by HTCC were investigated. The FT-IR and NMR results indicated that the substitution reaction mainly occurred on the amine groups of chitosan, and up to 90% substitution degree was obtained. Compared with chitosan, the solubility of HTCC was improved after modification. In addition, the crystallinity and the thermodynamic stability of silk fiber were improved after treated by HTCC solution, and the decomposition temperature increased from 318.93°C to 326.45°C. The antibacterial performance of silk fabrics to coli and staphylococcus were both significantly improved after treated by HTCC，and the inhibitory rate of silk fabrics had no significant decrease even though after soaping 30 times. Furthermore, the dyeing behaviors of silk fabrics to acid dyes and reactive dyes were improved, and the dyeing rate, the color fixing rate and the K/S value also increased.