A probabilistic method for sector congestion prediction taking into account wind uncertainty is presented. Firstly, the ensemble trajectory prediction method subject to the uncertainty of wind forecast and the analysis method of the uncertainty of flight time prediction are studied. The ensemble trajectory prediction method based on weather ensemble forecasts is used to obtain the set of predicted trajectory. According to the trajectory set, the uncertainty of the look-ahead time is statistically analyzed, and the regression prediction equation of the flight elapsed time spread is established with the look-ahead time, sector entry point and flight time as explanatory variables. Then the sector probabilistic congestion prediction method is studied to obtain the traffic demand prediction set based on the trajectory prediction set and then calculate the sector congestion probability and the expected capacity missing value of the sector. The effectiveness of the proposed method is verified by using European Centre for Medium-Range Weather Forecasts (ECMWF) ensemble forecast data and historical flight plan data for typical busy sectors in China. The probabilistic congestion prediction based on the proposed method is beneficial to improve the effectiveness of Air Traffic Flow Management (ATFM) strategy and reduce the workload of controllers.