Sub-beam concept is very useful for size reduction of multiple beam phased array antenna (PAA) systems that are applied for high-throughput communication satellites. In this paper, the synthesis procedure for a PAA with multiple sub-beams in two dimensions of the coverage domain is proposed and analyzed. In the design procedure, the interleaved sub-arraying technique has been applied to eliminate the grating lobes. The extremely short angular distance between adjacent sub-beams is challenging. An innovative beam forming network is proposed, which can generate multiple orthogonal sub-beams while keeping the required angular distance between sub-beams. To demonstrate the effectiveness of the design technique, an example considering the requirements derived from conceptual design of a high-throughput communication payload is presented. The array is optimized using the genetic algorithm while taking into account the technical requirements of the antenna. The gain patterns exhibit a 0.4° angular distance between adjacent sub-beams. In addition, the number of sub-arrays and element spacing guarantee the orthogonality of the sub-beams. The calculated carrier to interference ratio in the synthesized array shows that it has acceptable values in each spot. The aperture size reduction in the synthesized array compared to a conventional multiple beam array is more than 36.7%.