The invention discloses a cross-basin hydropower station group peak regulation optimization scheduling method considering a water abandoning risk. The method comprises the following steps of S1, constructing a hydropower station group peak regulation optimization scheduling model; S2, calculating the water abandoning risk of each cascade hydropower station; S3, coordinately distributing the generating capacity of each power station based on the water abandoning risk of each power station; and S4, calculating an optimal solution of the hydropower station group peak regulation optimization scheduling model based on the electric quantity distribution of each power station to obtain an output process line of each power station, and completing hydropower station group combined peak regulation scheduling. The hydropower station water abandoning risk is quantitatively analyzed through the runoff frequency. The peak shaving electric quantity of the hydropower station groups in different drainage basins is coordinated and distributed based on the water abandoning risk value, so that the water abandoning risk of each hydropower station can be fully considered, the runoff compensation and power compensation benefits of the hydropower station groups in different drainage basins are exerted, the hydropower water abandoning risk is greatly reduced during peak shaving of the power grid hydropower system, and the hydropower water abandoning electric quantity is reduced.