In this study, a pilot-scale tidal-flow paddy wetland system based on multifunctional coupling was constructed to treat land-based aquaculture tailwater of Macrobrachium rosenbergii. This study explored the purification ability, CH4 emissions, arthropod diversity, and comprehensive benefits of the tidal-flow paddy wetland system to provide a scientific basis for the application of this system. The results showed that the tidal-flow paddy wetland system could effectively purify land-based aquaculture tailwater. The removal capacities of dissolved inorganic nitrogen, total nitrogen, dissolved inorganic phosphorus, and total phosphorus were approximately 54.3%, 44.9%, 42.9%, and 43.0%, respectively. Simultaneously, the system had no negative impact on the external environment and indirectly purifies river water. Compared with conventional paddy fields, the tidal-flow paddy wetland system reduced CO2 and CH4 emissions by 5.4% and 92.5%, respectively. Compared to conventional paddy fields during the flooding period, the abundance of the mcrA gene in the tidal-flow paddy wetland decreased by 82.3%. Moreover, the tidal-flow paddy wetland system improved biodiversity and natural enemy abundance/pest abundance, inhibited pest outbreaks, supported more species, and increased comprehensive benefits compared to the control.