Filters are popularly used in municipal wastewater treatment plants (WWTPs) as the final guards against effluent solids; however, their impacts on antibiotic resistance gene (ARG) removal in the WWTPs are still unclear. In this study, metagenomic analysis was used to find out the distribution characteristics of ARGs in two WWTPs equipped with the same D-Type fiber filters. Samples of influent, activated sludge liquor, secondary clarifier effluent, and D-Type filter effluent were found to host 695, 609, 675, and 643 ARG subtypes, respectively. The detected ARGs mainly included macB (4.1–8.9%), sav1866 (1.7–3.4%), and oleC (1.6–3.8%). Co-occurrence network analysis combined with contribution analysis helped to identify the ARG-related risks in the samples. Microbacterium, Acinetobacter, Gordonia, and Streptomyces significantly correlated with more than ten kinds of ARG subtypes, implying that they are potential hosts for these resistance gene subtypes. The number of ARG subtypes in the D-Type filter was less than those in the secondary clarifier effluent, indicating the potential of D-Type filters to effectively reduce the ARGs released into the environment. However, the abundance of two pathogens, Mycobacterium and PmrA, increased after the treatment by the D-Type filter, which may reveal the adverse effects of intercepting ARGs inside the fibers. The results may help the understanding of the complex role of the D-Type fiber filter on ARG distribution in WWTPs.