Background/Objectives: The objective is to develop algorithms for improving Quality of Service with minimum delay and higher throughput using intelligent networking with cross layer architecture. Methods/Statistical analysis: For Mobile satellite communication Low Earth Orbit (LEO) satellites are used. Mobile satellite networks using LEO satellites provides less delay and high bandwidth. The cross-layer design is the method used to allow optimized operation in the modern heterogeneous wireless environment. Findings: The throughput improves with speed of transmission of information with cross layer design compared to the existing OSI model. The packet ratio increases with increasing transmission rate in comparison with the existing model. The overall delay is minimized in the proposed system with increase in number of packets. Simulation developed establishes that better QOS can be obtained with minimum delay and improved throughput in MSC networks using intelligent networking with cross layer architecture. Application/Improvements: The various applications of mobile satellite communication includes TV broadcasting, digital processing and point to point communication. The throughput is improved by 30% with speed of transmission of information. Packet ratio increases by 20% with increasing transmission rate. The overall delay is reduced by 17% with the help of cross layer design which is the optimized level compared to the existing model.