The invention discloses a microbial degradation ecological restoration method comprising the following steps: S1, exploring a river channel; S2, cleaning the surface of the river channel; S3, cleaning the bottom of the river channel; S4, detecting and treating; and S5, managing and monitoring. Bottom mud cleaned in the step S3 is accumulated to the two sides of the river channel, and a river shoal is formed; and aquatic plants and hygrophytes are planted on the river shoal, and ecological restoration treatment of the bottom mud is completed. According to the requirements of aquatic organisms for hydrology and habitat conditions, the river channel form is properly transformed, fish organisms in the original river channel are not damaged, meanwhile, proper aquatic organism varieties and microbial treatment agents are configured in different habitat areas, a river channel ecological system is effectively restored, the self-cleaning capacity of the river channel is improved, the biodiversity is recovered, and the function of an ecological system is improved; and meanwhile, the repaired river channel can be detected for a long time through the repairing method, and the river channel is prevented from being repeatedly polluted.