The invention discloses a two-dimensional scanning varactor active super-surface electromagnetic lens antenna, which comprises a focusing lens, a two-dimensional scanning array, gaskets, a support column, a horn antenna and a base. The focusing lens is a super-surface electromagnetic lens. The two-dimensional scanning array, the focusing lens and the support column are connected by the gaskets inturn. The two-dimensional scanning array is formed by superimposing two one-dimensional scanning arrays: an x-direction scanning array and a y-direction scanning array, wherein the y direction is usedas the polarization direction, the z direction is used as the axis-of-symmetry direction of the lens, and the bias lines of the varistors in the two one-dimensional scanning arrays are in the x direction. The antenna realizes two-dimensional scanning by changing the bias voltages of the varactors. The scanning array realizes two-dimensional scanning through the one-dimensional scanning arrays realized by two groups of varactor active super-surfaces, the scanning directions of the two arrays are orthogonal, and the two arrays are longitudinally superimposed. By using the method, the complexityand cost of super-surfaces in a large-scale two-dimensional scanning array can be reduced. Meanwhile, the focusing lens is realized by a super-surface, and the longitudinal size is reduced.