This study presents a simple method to immobilize β-agarase onto amino-modified magnetic nanoparticles (MNPs) by biotin/streptavidin (BT/SA) recognition. The effect of BT functionalized with different lengths of poly(ethylene glycol) (PEG) on the activity and stability of heterogeneous biocatalysts was also investigated. The results showed that the enzymatic activity was retained above 93% under the immobilization conditions (pH 7.0, 25 °C, 6 h, and β-agarase concentration of 1 mg/mL). The optimal pH and temperature for both free and immobilized β-agarases were 7 and 30 °C, respectively. PEG length played an important role in the catalytic performance of the immobilized enzyme. As the PEG length increased, an increased trend in activity retention and yield of neoagarobiose was observed. Ultimately, the introduction of PEG 24 improved the activity retention of immobilized β-agarase up to 135.67%, and retained 84.18 and 37.04% of residual activity after incubation for 6 h at 40 and 45 °C, respectively, while only 30.50 and 0% of residual activities were observed for free β-agarase at these temperatures, indicating the significantly enhanced stability of the β-agarase after immobilization. Additionally, β-agarase-BT PEG24 -SA@MNPs showed the highest yield of neoagarobiose at 45 °C, which was 1.89-fold higher than that of the free enzyme. These results indicated that immobilization of β-agarase on BT PEG -SA@MNPs improved both the catalytic efficiency and stability of the enzyme, thereby promoting the continuous production of neoagarobiose.