A liquid-cooling pump and a flow channel structure thereof are disclosed. The flow channel structure includes a liquid pump mounting chamber. A bottom of the liquid pump mounting chamber is centrally formed with a liquid inlet. A peripheral side of the liquid pump mounting chamber is formed with a liquid outlet. An inner wall of the peripheral side of the liquid pump mounting chamber is convexly provided with a protruding boss corresponding to one side of the liquid outlet and surrounding an impeller, and is concavely provided with a guide groove corresponding to another side of the liquid outlet and surrounding the impeller. The protruding boss is gradually thinned along a rotating direction of the impeller. The guide groove is gradually deepened along the rotating direction of the impeller and communicates with the liquid outlet.