Water scarcity severely constrains agricultural sustainability in arid and semi-arid Northwestern China, while the rapid expansion of livestock production generates large volumes of biogas slurry (BS) that require safe and efficient reuse. Delivering BS through subsurface drip irrigation (SDI) offers a promising route to couple irrigation and fertilization and to promote crop-livestock circular agriculture. However, the complex water quality of BS can accelerate emitter clogging, which remains a critical barrier to field-scale adoption. This study used a long-term in-situ field experimental platform to systematically investigate the clogging characteristics, formation mechanisms, and pathways of emitters in biogas slurry SDI systems. The feasibility of this system in arid northwestern regions was quantitatively evaluated, and targeted regulation strategies were proposed. Results showed that, the BSDI clogging remained below 25% at 150 h, supporting its technical feasibility for deployment in arid Northwestern China. Nevertheless, the biogas slurry's high suspended solids and substantial organic loading acted synergistically to enhance particulate deposition, inorganic scaling, and biofilm proliferation, ultimately inducing composite emitter clogging. Concurrently, water quality variations reshaped the structure of clogging-associated microbial communities and shifted predicted functional profiles (KEGG). Key taxa (e.g., Chloroflexaceae and Halocella) may potentially contribute to the acceleration of composite clogging within emitter labyrinths by enhancing carbohydrate metabolism, glycan biosynthesis, and nitrogen and phosphorus cycling. These functional shifts promote extracellular polymeric substance secretion and biofilm maturation, strengthen surface attachment, and increase particulate capture, thereby reinforcing the coupled processes of biofilm accumulation, particle deposition, and mineral scaling.