The shock wave drag influence from the section area distribution should be considered in supersonic aircraft design, and the aircraft configuration should be adjusted and optimized according to the area rule. To increase the efficiency of supersonic aircraft configuration adjustment, the accurate shape-modified method is researched through the analysis of aircraft section area distribution curve based on the area rule. An aircraft section area distribution curve analysis method is proposed based on automatic area rule judgment, which could automatically judge and locate the wave drag rising position. And then the fast computer-aided shape-modified method for aircraft fuselage configuration adjustment is given. With the method, the shape of the supersonic aircraft can be analyzed automatically and quickly, and the accurate section positions to be modified along with the adjusted suggestion of quantized section area are provided. The method is used in the fuselage configuration adjustment of a supposed supersonic bomber. Factors increasing the wave drag could be quickly discriminated and located with the method, including inflexions, steps, extremum and concave points on the section area curve. Manual modifications are conducted on the sections according to the adjustment suggestion, and then the drag coefficient is reduced 1.5%, which validates the effectiveness of the method.