Abstract: Constructed wetlands (CWs) have been widely recognized as an economical and eco-friendly technology for wastewater treatment, relying on the synergistic interactions among plants, substrates, and microorganisms to remove various pollutants, particularly nitrogen (N) and phosphorus (P). Among these, microbial communities play the central role in driving key biogeochemical processes such as nitrification, denitrification, and phosphorus accumulation. This review systematically summarizes the major functional microbial groups involved in N and P removal within CWs. For nitrogen removal, common taxa include Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria, which mediate ammonification, nitrification, and denitrification. However, conventional nitrogen removal pathways often face limitations such as inefficient nitrification under low temperature or oxygen, and insufficient carbon sources for denitrification. To address these challenges, five alternative nitrogen removal pathways suitable for low-carbon conditions are highlighted: partial nitrification-denitrification (saving 40% carbon), sulfur autotrophic denitrification (using reduced sulfur compounds as electron donors), denitrifying anaerobic methane oxidation (coupling methane oxidation with denitrification), heterotrophic nitrification-aerobic denitrification (single-step nitrogen removal under aerobic conditions), and anaerobic ammonium oxidation (anammox, using nitrite as electron acceptor). Their reaction principles, optimal conditions, and application potentials are compared. For phosphorus removal, although adsorption and precipitation by substrates dominate (>70% contribution), biological processes involving polyphosphate-accumulating organisms (PAOs), phosphate-solubilizing bacteria (PSB), and denitrifying PAOs also contribute significantly (10%-30%). The review further examines how vegetation and substrates shape microbial community structure and activity. Plants influence microorganisms through radial oxygen loss (creating oxic-anoxic microenvironments) and root exudates (providing carbon sources and signaling molecules). Different plant species (e.g., Phragmites australis, Typha orientalis, Myriophyllum spicatum) promote distinct microbial assemblages. Substrates affect microbial colonization, abundance, and diversity via their porosity, specific surface area, pH, and chemical composition. Natural materials (sand, zeolite, limestone), industrial by-products (slag, oyster shells), and manufactured media (activated carbon, biochar) each support different dominant functional groups, with composite or layered substrates often optimizing redox gradients and treatment performance. Finally, future research directions are proposed: elucidating the molecular mechanisms of key functional genes to enable targeted regulation of N/P removal; advancing engineering applications of alternative low-carbon pathways through technological integration, intelligent control, life-cycle economic assessment, and policy incentives; and establishing a ‘sensing-decision-regulation’ closed-loop system for real-time adaptive management of CWs under complex water quality conditions. This review provides a comprehensive understanding of microbial community characteristics in CWs and offers practical guidance for optimizing their design and operation for stable and efficient wastewater treatment.