The invention provides an ecological restoration system of water complement type river channel. The ecological restoration system of the water complement type river channel aims to overcome the shortcomings that a virtuous circle cannot be formed due to biological invasion, deterioration of water quality and the like since diverse ecological systems cannot be established in complement water type river channels in the prior art, and based on an existing water complement type river channel, an ecological river bed is constructed. The ecological restoration system includes the water complement type river channel, and an upstream water complement opening, an entrance deep pool, rock block groups, shoal and deep pool groups, an overflow dam, wooden pile groups, fish nests and biological channels, wherein the upstream complement water opening, the entrance deep pool, the rock block groups, the shoal and deep pool groups, the overflow dam, the wooden pile groups, the fish nests and the biological channels are arranged in the river channel; the entrance deep pool is arranged on the downstream part of the upstream complement water opening, the rock block groups are arranged on the downstream part of the entrance deep pool, the shoal and deep pool groups, the overflow dam, the wooden pile groups, the fish nests and the biological channels are arranged along the river channel in a distributed mode; and trees are planted on river channel slope protection, and water plants are planted in shoals. According to the ecological restoration system of the water complement type river channel, the biodiversity is restored, the water environment is improved, and using in the water complement type river channel is suitable.