The polymeric structure characteristics of β-chitosan from jumbo squid (Dosidicus gigas) pens and α-chitosan from shrimp shells during depolymerization by cellulase hydrolysis at different degrees of deacetylation (DDA) (60, 75, and 90%) were investigated by using Fourier transform infrared spectroscopy and X-ray diffraction. Antibacterial activity of β-chitosan against Escherichia coli and Listeria innocua was compared with that of α-chitosan at similar Mw and degrees of deacetylation (DDA) by studying inhibition ratio and minimal inhibition concentration (MIC) and was coordinated with the structural characteristics of the two forms of chitosan. β-Chitosan was more reactive to cellulase hydrolysis than α-chitosan due to its relatively lower crystallinity (CI) and loose crystal property, and the 75% DDA chitosan was more susceptible to cellulase than the 90% DDA ones with the 75% DDA of β-chitosan mostly reactive. Both forms of chitosan showed more inhibition against E. coli than against L. innocua, and no difference against L. innocua between the two forms of chitosan was observed. However, the two forms of chitosan exhibited different levels of antibacterial activity against E. coli, in which 75% DDA/31 kDa β-chitosan demonstrated significantly higher inhibition (lower MIC) than that of 75% DDA/31 kDa α-chitosan, whereas 90% DDA/74-76 kDa α-chitosan had a higher inhibition ratio than that of 90% DDA/74-76 kDa of β-chitosan. This result may be explained by the impact of the different structural properties between α- and β-chitosan on chitosan conformations in the solution. This study provided new information about the biological activities of β-chitosan, a bioactive compound with unique functionalities and great potential for food and other applications.