The invention provides a fault early-warning method and system for a wind turbine generator set variable propeller system. The fault early-warning method comprises the steps that historical data of the variable propeller system running normally and pitch angles changing are collected, and the historical data comprise the pitch angle of each blade in the variable propeller system; filtering processing is performed on the historical data, and the data deviation range is confirmed according to the data deviation before and after the filtering processing; and the filtering processing is performedon the data to be measured of the variable propeller system, and when the data deviation before and after the filtering processing exceeds the data deviation range, fault early-warning is sent out. Bymeans of the fault early-warning method and system for the wind turbine generator set variable propeller system, the fault early-warning can be performed when the variable propeller angle does not generate obvious abnormality in the early stage of variable propeller system fault aiming at the situation of a variable propeller angle curve being not smooth, and the early variable propeller fault isdetected.