Height measurement of meter wave radar is a difficult and important problem. This paper studies the height measurement of meter wave polarimetric (MWP)-MIMO array radar under complex terrain. The traditional electrically short dipole has low radiation efficiency, and the collocated dipole vector antenna has strong mutual coupling. This paper proposes to use electrically long dipoles and separated vector antennae to solve the problems of low radiation efficiency and strong mutual coupling. In addition, different from the traditional flat terrain, the research of this paper is based on the conditions of complex undulating terrain. First, the height measurement signal model of the MWP-MIMO radar with separated electrically long dipole under the complex terrain is derived. Then, a preprocessing method of block orthogonal matching pursuit is proposed to obtain the coarse estimation of the target’s elevation. Then, under the guidance of the coarse estimation, the generalized MUSIC algorithm is used to obtain the high-precision elevation estimation of the target, and then the height measurement of the target is obtained according to the geometric relationship. Finally, the effectiveness of the proposed algorithm is proved by computer simulations.