The invention discloses a two-dimensional DOA (Direction of Arrival) estimation method based on rooting Capon. The method comprises the following steps of: firstly, receiving signals by double parallel arrays and sampling the signals; secondly, solving a covariance matrix for the sampled signals to obtain a two-dimensional Capon spatial spectrum function related to the covariance matrix; thirdly, taking an improved formula of a denominator of the spatial spectrum function as a cost function of a rooting Capon algorithm, and converting the cost function into a one-dimensional polynomial; and finally, rooting the one-dimensional polynomial, and obtaining the elevation angle and the azimuth angle of the automatically paired signal source by using the corresponding relation of the two-dimensional angles. According to the method, the problem of huge calculation amount caused by spectral peak search of a two-dimensional Capon algorithm is solved, meanwhile, the advantage that the Capon algorithm does not need priori information of the information source number is inherited, DOA estimation time is shortened, the estimation efficiency of the information source direction is effectively improved, and the method can be well applied in practice.