The invention discloses a flexible DC configuration method and system for suppressing two-DC simultaneous commutation failure. The method comprises steps that multiple subareas of the grid and transmission sections among the subareas are determined; fault checking is performed, and a first AC fault area causing two-DC simultaneous commutation failures is determined; a flexible DC configuration candidate line set between two converter stations is determined; electrical distances among high voltage buses of two DC receiving inverter stations are respectively calculated on the condition that flexible DC is mounted in different lines; the electrical distances are arranged in descending order, a line configuration order set of the flexible DC is determined, and lines in the line configuration order set are respectively sequentially selected as the current line; the flexible DC is mounted in the current line, fault checking is further performed, and a second AC fault area is determined; a commutation failure suppression effect index is calculated, the commutation failure suppression effect index is compared with the preset index threshold, and a flexible DC configuration scheme is determined on the basis.