In this study, chitooligosaccharide-niacin acid conjugate was designed and synthesized through the reaction of chitooligosaccharide and nicotinic acid with the aid of N,N′-carbonyldiimidazole. Its cationic derivatives were prepared by the further nucleophilic substitution reaction between the chitooligosaccharide-niacin acid conjugate and bromopropyl trialkyl ammonium bromide with different alkyl chain lengths. The specific structural characterization of all derivatives was identified using Fourier Transform Infrared Spectroscopy (FTIR) and Nuclear Magnetic Resonance (NMR), and the degree of substitution was obtained using the integral area ratio of the hydrogen signals. Specifically, the antibacterial activities against Escherichia coli, Staphylococcus aureus, Pseudoalteromonas citrea and Vibrio harveyi were evaluated using broth dilution methods. In addition, their antifungal activities, including Botrytis cinerea, Glomerella cingulate and Fusarium oxysporum f. sp. cubense were assayed in vitro using the mycelium growth rate method. Experimental data proved that the samples showed antibacterial activity against four pathogenic bacteria (MIC = 1–0.125 mg/mL, MBC = 8–0.5 mg/mL) and enhanced antifungal activity (50.30–68.48% at 1.0 mg/mL) against Botrytis cinerea. In particular, of all chitooligosaccharide derivatives, the chitooligosaccharide derivative containing pyridinium and tri-n-butylamine showed the strongest antibacterial capacity against all of the test pathogenic bacteria; the MIC against Vibrio harveyi was 0.125 mg/mL and the MBC was 1 mg/mL. The experimental results above showed that the introduction of pyridinium salt and quaternary ammonium salt bearing trialkyl enhanced the antimicrobial activity. In addition, the cytotoxicity against L929 cells of the chitooligosaccharide derivatives was evaluated, and the compounds exhibited slight cytotoxicity. Specifically, the cell viability was greater than 91.80% at all test concentrations. The results suggested that the cationic chitooligosaccharide derivatives bearing pyridinium and trialkyl ammonium possessed better antimicrobial activity than pure chitooligosaccharide, indicating their potential as antimicrobial agents in food, medicine, cosmetics and other fields.