The invention belongs to microbial water body restoration, and particularly relates to a microbial agent for treating a black and odorous water body in complicated closed conduits and application thereof. The microbial agent is prepared by mixing 15 to 30 weight parts of enterococcus faecalis, 5 to 10 weight parts of lactobacilli, 25 to 50 weight parts of bacilli and 5 to 10 weight parts of saccharomycetes through fermentation. The compound efficient microbial agent and micro-nano bubbles synchronously and gradually flow from branch streams to trunk streams of the closed conduits; in the process, bioactive substances, oxygen bubbles and riverway suspended matters or suspended bottom mud are sufficiently mixed; mixtures are fast adsorbed onto suspended particles; pollutants of the water body are degraded through the biological metabolism process; and the blackness and the odor of the water body are reduced, so that the quality of the water in the complicated closed conduits is effectively improved.