The classical flexible mattress has been widely used in waterway regulation engineering because of its advantage in protecting river beds. However, its disadvantage is the lack of ecological functions. Therefore, to optimize the classical flexible mattress, a new flexible mattress with ecological cavities was developed by waterway regulation designers. Flow patterns around the cavities were precisely measured by a 3D velocity meter in a flume. The results indicated that the velocity and turbulence intensity rapidly decreased when the fluid flowed into the cavities. Furthermore, the decay rate in the velocity-stable region reached 89% and the average vertical velocity in the cavity was only 10% of the bottom velocity in the upper surface. The profile of the vertical velocity was adjusted to the law of “large in the middle, small at the upper and bottom ends”, and the peak value of the turbulence intensity was near the ceiling of the cavities. The bottom velocity of the cavity in the velocity-stable region was lower than the incipient velocity of the bed material load, thereby creating a favorable hydraulic condition and thus achieving the ecological benefits of little deposits. The findings of this study provide a reference for the design and application of the flexible mattress with ecological cavities.