MRDS is a short range missile/rocket defense system which protects a main battle tank(MBT) from threats in a short range. It is composed of 2 radars, 2 infrared trackers(IRTs), 1 fire control computer(FCC), 2 launchers and countermeasures. To guarantee the performance of the MRDS, these components have to be mounted on the vehicle with the known positions and directions and it is required to compensate the alignment errors. In this paper, a system alignment method using angular error compensation is proposed to install its components within a tolerance on the MBT. The test results are presented to evaluate and verify the effectiveness of the proposed method.