The water-level fluctuation zone (WLFZ) experiences severe soil erosion in the Three Gorges Reservoir area. Despite the single effect of vegetation and gravel play significant roles in dissipating energy and reducing wave erosion, their synergistic effect have been proven to be more effective. However, the ecological adaptation and compatibility of gravel mulching with Cynodon dactylon, a typical plant species in this zone, remain poorly characterized. This study addressed this knowledge gap through pot experiments examining nine combinations of three gravel particle sizes (5–10, 10–15, and 15–20 mm) and three gravel coverage thicknesses (20, 40, and 60 mm), using bare soil conditions without gravel set as the control check (CK) group. Potted trials with Cynodon dactylon were conducted under these conditions, and precision maintenance protocols were carried out during the seedling stage, followed by autonomous regulation under natural conditions. Soil physicochemical properties, plant growth and physiological parameters were systematically monitored at four temporal intervals (30, 90, 180, and 360 days) to quantify evolutionary patterns. Furthermore, the ecological adaptation and compatibility of gravel mulching with Cynodon dactylon was quantitatively assessed by using the entropy weight method. The results indicated that gravel mulching improved the physical and chemical properties of the soil, compared with the CK group, the soil bulk density and electrical conductivity decreased by 1.53%—4.13% and 1.03%—19.18%, the porosity increased by 1.00%—4.63%, the soil organic matter, total nitrogen, total phosphorus, available nitrogen content and available phosphorus content exhibited average variation of -6.89%—10.33%, 0.58%—17.25%, -14.51%—6.06%, -34.53%—1.96% and 5.22%—45.17%. The gravel mulching generally exerted an inhibitory effect on plant growth. The plant height, aboveground and underground biomass of Cynodon dactylon decreased by 14.04%—30.44%, 25.69%—53.51%, and 49.62%—75.49%, the chlorophyll content, soluble sugar content, net photosynthetic rate, transpiration rate, stomatal conductance, and intercellular CO2 concentration exhibited an average variation of -5.68%—17.03%, -28.42%—3.70%, -54.95%—-31.90%, -50.45%—-20.30%, -44.85%—-15.56% and -27.65%—-8.42%. The entropy weight analysis showed that gravel mulching significantly inhibited plant growth and development processes, with the weights of plant physiological growth indicators exerting greater influence than those of soil indicators. The optimal ecological adaptation and compatibility condition for Cynodon dactylon growth was observed when the gravel layer was characterized by the particle size of 5—10 mm and the thickness of 20 mm. These findings deliver a scientific foundation for implementing synergistic engineering-ecological restoration strategies in the WLFZ.