The invention discloses an efficient cross-flow type water turbine generator set with a cleaning function. The efficient cross-flow type water turbine generator set comprises an S-shaped water pipe, a spindle, a flow guiding mechanism, a runner chamber, a sealing mechanism, a power generating mechanism, a cleaning mechanism, a detection mechanism and a control mechanism. The cleaning mechanism comprises a high-pressure water pump and an electronic control valve, wherein the electronic control valve is arranged on a water inlet pipe of the high-pressure water pump, the water inlet pipe of the high-pressure water pump is connected with an inlet of the S-shaped water pipe, and a water conveying pipe of the high-pressure water pump is connected with the runner chamber. A water throwing cup is arranged outside the sealing mechanism. The detection mechanism comprises a water flow sensor, a rotating speed sensor and a flow meter. According to the efficient cross-flow type water turbine generator set, the sediment attaching condition on a runner can be judged according to the rotating speed of the runner so that timely treatment can be achieved, and power generating efficiency is improved; the waterproofness can be detected according to the flow of water drainage of the water throwing cup, an alarm can be used for reminding workers to treat and overhaul the water turbine generator set in time, and corrosion and the safety problem of the power generating mechanism are avoided.