This paper presents the results of an analysis of the sensitivity of the use of a variable noise reduction system (VNRS), considered in the new landing and takeoff (LTO) noise standard for supersonic aircraft, using a Japan Aerospace Exploration Agency (JAXA)-designed 66-ton twin-engine conceptual low-boom supersonic airliner as an example. The analysis was conducted using a tool developed by JAXA and examined the sensitivity of low-speed aerodynamic performance, the sensitivity of takeoff reference speed, the sensitivity of thrust control and flap control duration time ranges, and the sensitivity of noise level to takeoff profile uncertainty. The analyses showed that improving low-speed aerodynamic performance and increasing the takeoff reference speed significantly impact noise levels and the use of VNRS could reduce noise by 2.1 EPNLdB while maintaining the performance of the aircraft. Because the effective noise reduction method by changing the takeoff procedure considered differs for each noise measurement point, it is important to design a takeoff procedure that incorporates an appropriate VNRS. Uncertainty of the takeoff profile was also investigated using Monte Carlo simulations, and it was shown that noise reduction by VNRS is effective even with the assumed uncertainty in the takeoff profile.