Tidal flats are one of the main types of coastal wetlands in the world. Benthic organisms, which accommodate in tidal flats, playing an important role in regulating the ecological environment. Benthic microalgae can interacts with sediment and hydrodynamic process, driving the development of micro-geomorphic patterns in tidal flats. It is very important to clarify the effect of benthic organisms on the evolution of micro-geomorphic patterns in tidal flats. In this paper, taking the tidal flat in the Yellow River Delta wetland as a study area, by constructing a micro-geomorphic dynamic model, we explored the effect of benthic organisms on the evolution of the micro-geo micro-geomorphic microtopographic system. The results show that (1) under the interaction of the benthic microalgae growth, sediment diffusion and water flow redistribution, a regular micro-geomorphic pattern of microalgae-covered hummocks alternating with water-filled hollows is formed. (2) The formation of micro-geomorphic pattern improves the primary productivity and sediment elevation in the flat tidal ecosystem. (3) Microalgal biomass and sediment elevation in the micro-geomorphic system respond nonlinearly to erosion disturbance, the system has tipping points and bistable states within a certain range of erosion rate. (4) The invasion of mud snails in the Yellow River estuary reduces the stability of the micro-geomorphic system to erosion disturbance, and the stability of system decreases with the increase of mud snail biomass.