A multidisciplinary optimization (MDO) method has been developed to design a computational fluid dynamics (CFD)-based low-boom configuration that can be obtained from a Pareto solution of a low-fidelity multi-objective MDO problem with mission constraints. This paper refines the developed MDO method by using multifidelity models for CFD-based multi-objective MDO and a better method for the system-level trade between the target low-boom ground noise level and the overland range. The refined MDO method can generate a low-boom configuration that satisfies the mission requirements, has the lowest takeoff gross weight and the longest range for the low-boom mission, trims the low-boom cruise flight with fuel redistributions, and has a reversed equivalent area distribution closely matching a low-boom target with ground noise level below 70 perceived level in decibels. The validity of the refined MDO method is demonstrated by a design study of a low-boom supersonic transport that carries 40 passengers, flies a low-boom mission with cruise Mach of 1.7 and range of 3500 n mile, and cruises overwater at Mach 1.8 with range of 3882 n mile. Moreover, the refined MDO method eliminates the difference between the assumed cruise weight for CFD-based low-boom inverse design optimization and the estimated cruise weight of the optimal inverse design solution with respect to the mission requirements.