Residual antibiotics in swine wastewater promote the proliferation of the antibiotic resistome, posing significant threats to environmental and human health. Although anaerobic digestion (AD) is widely applied for treating swine wastewater, the effects of antibiotics on the microbial community and resistome during AD remain unclear. This study employed amplicon and metagenomic sequencing, combined with long- and short-read hybrid assembly, to comprehensively investigate the impact of sulfonamides on the microbiome and resistome during AD. Enterococcus, a genus capable of utilizing exogenous folate, was identified as the dominant genus under sulfonamide stress. A total of 24 antibiotic resistance gene (ARG) types and 440 subtypes were identified. Sulfonamide stress selectively enriched sulfonamide resistance genes, with no notable co-selective effects on ARGs for other antibiotic classes. Short-term exposure significantly enriched sul2 (3.8-fold) and sul3 (4.0-fold), while long-term exposure enriched sul1 (1.6-fold). Sulfonamides especially promoted the proliferation of sulfonamide resistance genes on both mobilizable and non-mobilizable plasmids. The co-occurrence of multiple categories of mobile genetic elements and ARGs on contigs was inferred to play a critical role in driving ARG dissemination. Whereas a strain belonging to Enterococcus_I emerged as the dominant resistant bacterium in the AD system, a particular multidrug-resistance risk was identified for a strain belonging to the Filifactoraceae family. This work provides a new perspective on the impact of antibiotics on microbial community and antibiotic resistome composition and dynamics during the AD treatment process of swine wastewater.