Background Carboxyl-functionalized magnetic nanoparticles were synthesized via chemical co-precipitation method and modified with oleic acid which was oxidized by potassium permanganate, and κ-carrageenase from Pseudoalteromonas sp. ASY5 was subsequently immobilized onto them. The immobilization conditions were further optimized, and the characterizations of the immobilized κ-carrageenase were investigated. Results The κ-carrageenase was immobilized onto magnetic iron oxide nanoparticles, and the bonding was verified by Fourier transform infrared spectroscopy. The optimal conditions for κ-carrageenase immobilization were 2.5% (w/v) glutaraldehyde, 13.9 U κ-carrageenase for 20 mg of magnetic nanoparticles, a 2-h cross-linking time, and a 2-h immobilization time at 25°C. Under these conditions, the activity of the immobilized enzyme and the enzyme recovery rate were 326.0 U · g- 1 carriers and 46.9%, respectively. The properties of the immobilized κ-carrageenase were compared with those of the free enzyme. The optimum temperatures of the free and immobilized κ-carrageenase were 60 and 55°C, respectively, and the optimum pH of κ-carrageenase did not change before and after immobilization (pH 7.5). After immobilization, κ-carrageenase exhibited lower thermal stability and improved pH stability, as well as better storage stability. The immobilized κ-carrageenase maintained 43.5% of the original activity after being used 4 times. The kinetic constant value (Km) of κ-carrageenase indicates that the immobilized enzyme had a lower binding affinity for the substrate. Conclusions Under optimal conditions, the activity of the immobilized enzyme and enzyme recovery rate were 326.0 U · g- 1·κ-carrageenase-CMNPs and 46.9%, respectively. The thermal, pH, and storage stabilities of κ-carrageenase-CMNPs were relatively higher than those of free κ-carrageenase.