To investigate entropy generation caused by a grooved structure on flow, we used Fluent software and large eddy simulation (LES) technology to analyze entropy generation in flow over a plate with a grooved structure. It showed that a grooved structure was able to reduce entropy generation in the flow. At 30 m·s^-1(Re≈20 000), total entropy generation in near-wall region decreased by approximately 25%. And at 40 m·s^-1(Re≈27 000), it decreased by approximately 19%. However, the grooved structure did not have a sustained effect on subsequent flow. As distance from the wall in the normal direction increased, the effect decreased gradually. Entropy production at the top of the trench is much greater. And entropy production caused by turbulence is dominant. It provides a theoretical basis for optimizing drag reduction of trench structures.