Immobilized fillers have been increasingly utilized in biotrickling filters (BTFs) due to their positive impact on shock load resistance and recovery performance. However, due to the inherent characteristics of its immobilized carrier, the immobilized filler is prone to swelling during the long-term operation of the system, resulting in increased pressure drop. Polyurethane (PU) sponge was used as the cross-linked skeleton of immobilized filler and compared with direct emulsified cross-linked immobilized filler for treating ethylbenzene gas. In the early stage, both fillers can maintain good performance despite changes in the inlet concentration and short-term stagnation. However, on the 107th day of operation, the immobilized filler experienced swelling, and the pressure drop sharply increased to 137.2 Pa, while the PU immobilized filler was still able to maintain a low-pressure drop level. The results of the microbial diversity analysis revealed that the microbial community structure of PU immobilized fillers remained relatively stable when responding to the fluctuations in operating conditions. PU sponges as the skeleton can effectively prolong the service life of the immobilized filler and improve the performance of the biotrickling filter.