In this study, the alginate/chitosan composite aerogels based on electrostatic interactions and noncovalent crosslinking were fabricated using sol-gel method followed by freeze-drying process. The solution property results showed that with the addition of chitosan in alginate solution, a tighter network was induced by the more entangled molecular chains. The aerogel morphology observations showed that the pore diameter decreased with the increasing weight ratio of chitosan in the aerogels, but was even much lower after the crosslinking of excess alginate with calcium ions. After crosslinking, the aerogels presented the improved thermal stability and higher mechanical properties, as well as stronger antibacterial activities against Staphylococcus aureus and Escherichia coli. Therefore, the enhanced physical and antimicrobial properties of the alginate/chitosan aerogels may be achieved by modulation of electrostatic interactions and noncovalent crosslinking, suggesting the promising applications of these composite aerogels as active food packaging materials for antimicrobial purpose. •A tighter network between chitosan and alginate was induced by electrostatic interactions.•The pore diameter of aerogels was much lower after noncovalent crosslinking with calcium ions.•Higher thermal stability, mechanical properties, and antibacterial activities were obtained.