In indoor scenario, radar echoes are interfered by clutter from walls, ceilings, floors, and other indoor objects. Therefore, clutter suppressing is one of the key problems for indoor radar. This paper focuses on the problem of clutter suppressing for a secondary radar system which can be used in indoor localization. A clutter suppressing method based on orthogonal polarization character is presented. The orthogonal polarization character here is achieved by a designed transceiver, which can transpond electromagnetic waves in vertical polarization if and only if the received signal is in horizontal polarization. Thus the newly introduced polarization character can be used to discriminate target from clutter. Clutter is suppressed after calculating scattering similarity parameters via Pauli decomposition. Simulations and an experiment are conducted to demonstrate the proposed method. Compared with previous methods, the proposed method can distinguish stationary target with both static and varying clutters. Therefore, it is more practical for applications.