Developing sodium alginate (SA)/chito-oligosaccharide (COS) beads with antibacterial properties is highly appealing for food industrial applications. Herein, in this paper, the different viscosity-average molecular weight of SA/COS polyelectrolyte (SCP) gel beads were prepared by adding a low concentration of calcium ions (Ca2+) as crosslinker and their size, mechanical property, microscopic morphology, elemental composition, and thermal stability of the gel beads were characterized. Furthermore, the morphological changes of gel beads in in vitro simulated digestion were investigated. A time-dependent co-culture assay was used to explore the antibacterial effect of gel beads on Staphylococcus aureus and Escherichia coli. The results showed that as the viscosity-average molecular weight (Mv) of SA decreased, the bursting strength faded, the thermal stability decreased, and the swelling index increased. Similarly, increasing the Ca2+ content could also regulate the characteristics of the gel beads, such as diminishing size, increasing the bursting strength, making the surfaces rough, and producing the network structure in the cross-section. In addition, Ca2+ competes with COS in cross-linking with the carboxyl groups of SA, which leads to a decrease in the content of N element on the surfaces of the gel beads and to a weakening of the antibacterial effect. After the addition of COS, the gel beads obtained antimicrobial effects and a denser cross-sectional structure. The present study could provide a theoretical basis for the design and development of novel gel foods in the food industry. Display omitted •Edible gel bead was made of sodium alginate (SA) and chito-oligosaccharide (COS).•With the addition of Ca2+, the network structure inside the gel beads appeared.•Ca2+ would compete with the COS for the binding site of SA.•The addition of COS endows the gel bead with excellent antimicrobial activity.