The Chinese Ocean Salinity Satellite is designed to monitor global sea-surface salinity (SSS). One of the main payloads onboard the Chinese Ocean Salinity Satellite, named the Interferometric Microwave Radiometer (IMR), is a two-dimensional interferometric radiometer system with an L-band, Y-shaped antenna array. The comparison of two different array orientations is analyzed by an end-to-end simulation based on the configuration of the IMR. Simulation results of the different array orientations are presented and analyzed, including the brightness temperature (TB) images, the distribution of the incidence angles in the field of view, the TB radiometric resolutions, the spatial resolutions, the number of measurements in the Earth grid and the expected SSS accuracy. From the simulations we conclude that one of the array orientations has better performance for SSS inversion than the other one. The advantages mainly result in wider swath and better SSS accuracy at the edge of the swath, which then improve the accuracy of the monthly SSS after averaging. The differences of the Sun’s effects for two different array orientations are also presented. The analysis in this paper provides the guidance and reference for the in-orbit design of the array orientation for the IMR.