In a natural basin, the vegetation can change the slope convergence and affect the surface runoff. Vegetation height may vary in an area, showing a two-layer combination of high and low collocation. This study aimed to understand the effects of double-layer vegetation in different submerged states on flow resistance. Plantings of vegetation at different heights may control landslides and contribute to soil and water conservation. This study explored the water flow resistance characteristics of double-layer vegetation at different heights. A plastic bar was used to simulate rigid vegetation, and an indoor channel fixed bed experiment was used to simulate vegetation with different heights of 5 cm and 7 cm, 5 cm and 8 cm, 5 cm and 9 cm, and 5 cm and 10 cm. By analyzing the relationship between the Darcy–Weisbach resistance coefficient (f) and water depth (h), it was concluded that when the vegetation is in a non-submerged state, f and h satisfy f= 5.6427 h+ 0.0245. When the water depth just submerges the low vegetation, f changes abruptly, and f and h satisfy the relationship f= 3.4075 h + 0.0021. When the water depth is the same as the height of high vegetation, f attains the maximum value. In addition, the flow resistance f increases by 0.03 with a 1 cm increase in the vegetation height h. When the vegetation is completely submerged, f is negatively correlated with h.