Elodea nuttallii (EN) is widely used in Chinese mitten crab (CMC) rearing practice, but it is not a native aquatic plant and cannot endure high temperature. Thus, large EN mortality and water deterioration events could occur during high temperature seasons. The aim of this study was to identify the use of local macrophytes in CMC rearing practice, including Ipomoea aquatic (IA) and Oryza sativa (OS). A completely randomized field experiment was conducted to investigate the crab yield, water quality, bacterioplankton community and functions in the three different systems (EN, IA, and OS). Average crab yields in the different macrophyte systems did not differ significantly. The IA and OS systems significantly decreased the TN and NO 3-N quantities in the outflow waters during the rearing period compared to the EN system, and the IA and OS plants assimilated more nitrogen than the EN plant. Moreover, the significant changes of bacterioplankton abundances and biodiversity in the three systems implied that cleanliness of rearing waters was concomitantly attributed to the differential microbial community and functions. In addition, principle component analysis successfully differentiated the bacterioplankton communities of the three macrophytes systems. Environmental factor fitting and the cooccurrence network analyses indicated that pH was the driver of bacterioplankton community structure. Functional predictions using PICRUSt (v.1.1.3) software based on evolutionary modeling indicated a higher potential for microbial denitrification in the IA and OS systems. Notably, the OS plants stopped growing in the middle of the rearing period. Thus, the IA system rather than the OS system could be a feasible and environmental-friendly alternative to the EN system in CMC rearing practice.