The invention discloses a method and system for detecting two-dimensional CFAR of a monopulse radar based on an FPGA. The method comprises the following steps of: A, designing a data pool, wherein thesize of the data pool is X*Y, X is a distance dimension, Y is the size of a reference window, a protection unit is set to be H, a detection factor is F, and a threshold is Z; B, judging whether a detection point is a boundary point or not, if not, executing C1, otherwise, executing C2; C1, calculating the comparison result of the energy values of the detected data in the upper direction, the lower direction, the left direction and the right direction, accumulating and multiplying F, comparing the product with Z, and if the product exceeds Z, taking the detected point as a target point; C2, dividing the upper direction, lower direction, left direction, and right direction of the detection unit into effective directions and invalid directions, wherein the number of the effective directionsis p; updating a threshold Z to p/4; calculating the comparison result of the energy value of the detected data in the effective directions, accumulating and multiplying F, comparing the product withZ, and if the product exceeds Z, taking the detected point as the target point. The method can effectively reduce false alarm; and the detection can be quickly and timely carried out when the reference window is larger.