Algal oligosaccharides (AOS) have been shown to effectively promote plant growth. While there have been many studies on the use of AOS in promoting crop growth, few have investigated their potential in improving ecological floating bed wastewater treatment. Therefore, this paper aims to explore the effects and mechanisms of AOS in enhancing ecological floating bed wastewater treatment. Water spinach was cultivated in aquaculture wastewater treated with varying concentrations of AOS (0.025, 0.05, 0.1, and 0.2 mg/L), with an ecological floating bed without AOS serving as the control group. Results shows the addition of AOS can significantly enhancing ecological floating bed plant and microbial accumulation, resulting in profound improvement in ecological floating bed wastewater treatment efficiency. This is evident in the increased plant height, stem diameter, main root length, number of roots, leaf area, above water-surface fresh weight, below water-surface fresh weight, above water-surface dry weight, below water-surface dry weight, chlorophyll a, chlorophyll b, and chlorophyll content. The combination of 0.05 mg/L AOS with the ecological floating bed exhibits the most favorable results, with percentage increases in various indicators were 44.0%, 52.9%, 29.9%, 62.0%, 28.0%, 141.6%, 84.0%, 97.7%, 220.0%, 24.6%, 34.2%, 26.9% compared to the control group. The addition of AOS to the water spinach ecological floating bed system significantly enhances the removal efficiency of water turbidity, chemical oxygen demand (COD), ammonia nitrogen (NH4⁺-N), nitrate nitrogen (NO3⁻-N), total nitrogen (TN), and total phosphorus (TP) water quality indicators. This experiment also investigated the differences in microbial community structure between the control group and the group with the optimal concentration of AOS to study the mechanism of action of AOS. The combination of 0.05 mg/L AOS with the ecological floating bed demonstrates the optimal removal efficiency. This study offers crucial technical insights for further optimizing ecological floating bed technology and improving water purification efficiency.