A hypersonic vehicle refers to an aircraft capable of sustained flight at Mach numbers greater than 5, powered by air-breathing engines or combined-cycle propulsion systems, operating within and across atmospheric layers (Liu 2004). Recognized as the third revolutionary advancement in aviation history following propeller and jet aircraft, it represents a critical development trend in aerospace for the 21st century. The exhaust nozzle, as the primary thrust-generating component of the engine, has been shown to contribute approximately 70% of total engine thrust at Mach 6 (Grarnland and Berens 1995). Thus, nozzle design quality directly impacts overall engine performance. Among nozzle configurations, the Single Expansion Ramp Nozzle (SERN) facilitates integrated propulsion-airframe design and is currently considered the optimal exhaust system for hypersonic vehicles. The SERN employs a highly integrated configuration between the vehicle aft-body and nozzle. While demonstrating excellent thrust coefficients at hypersonic speeds, its performance degrades significantly during transonic phases due to reduced nozzle pressure ratios. Under severe over-expansion conditions, the upper ramp surface not only fails to generate thrust but may even produce drag, leading to substantial deterioration of thrust coefficients (Christopher and Jaime 1991). Improving SERN performance at low Mach numbers has thus become a critical scientific challenge in hypersonic propulsion system integration. To address this, this chapter investigates SERN contour design and flow mechanisms for series- and parallel-configured TBCC engines. It explores active flow control via high-pressure secondary flow injection and passive flow control using cavity-based structures to enhance performance during over-expansion. The study further examines how key parameters of these active and passive control methods influence SERN performance and flow characteristics.