The water level fluctuation zone of the Three Gorges Reservoir has been affected by a number of ecological problems, most importantly, the loss of previous vegetation. The revegetation of this region is just one example of a potential solution to this issue, and revegetation projects have been carried out in the region over recent years in an attempt to restore the riparian ecosystem within the Three Gorges Reservoir region. The riparian species Hemarthria altissima and Cynodon dactylon have been commonly used in this revegetation effort. Knowledge of the growth responses of plant species to different flood regimes and identifying a suitable planting pattern will lead to improvements in the design of wetland management strategies. Therefore, the aim of this study was to determine the optimal planting pattern for these two species under different flood conditions. Four flooding conditions were designed using an independent-group design and their results were evaluated. These groups were the Control Group (CK), the Flooding-Dry Alternating Group (FD), the Soil-Flooding Group (FL), and the Submergence Group (SM). These groups had four different planting densities, which were 1, 2, 4, or 12 plants per experimental pot. Single cropping strategies were applied to the pot with one plant, while both single and mixed cropping strategies were applied to the pots with, 2, 4, and 12 plants. The ratio of H. altissima to C. dactylon in the mixed intercropping groups was 1:1 in the pots with 2, 4, and 12 plants. The results indicated that the total and aboveground biomasses of H. altissima and C. dactylon were significantly influenced by water treatment, planting density, and planting pattern (P < 0.05). The total and aboveground biomasses of C. dactylon significantly decreased in the mixed intercropping pots with medium and high planting densities under the CK and FD conditions (P < 0.05). In contrast, the total and aboveground biomasses of H. altissima increased in the mixed intercropping pots for all planting densities, and increased significantly at the high planting density under the CK and FD conditions (P < 0.05). The total H. altissima and C. Dactylon biomasses increased in the mixed intercropping pots with low and medium planting density under the FL treatment. The total and aboveground C. dactylon biomasses also significantly increased in the mixed intercropping pots with low and medium planting density under the SM treatment (P < 0.05). However, the mixed intercropping pattern with low and medium planting density did not influence the H. altissima biomass under the SM treatment (P > 0.05). Furthermore, the mixed intercropping pattern with high planting density did not influence the H. altissima and C. Dactylon biomasses under the SM treatment (P > 0.05). The inhibition influence of the mixed intercropping pattern to C. Dactylon declined as flooding stress increased. The results suggested that the long-term coexistence of H. altissima and C. Dactylon would improve if a mixed intercropping pattern with low and medium planting densities was adopted in areas where flooding lasted for a long period. Therefore, in order to strengthen the soil retention functions of H. altissima and C. dactylon, and improve the species diversity and community stability of the vegetation restoration, mixed intercropping with a high H. altissima-to-C. dactylon planting density is the optimal choice in low-altitude areas that are completely flooded.