This paper introduces a low-boom aircraft optimization design method guided by equivalent area distribution, which effectively improves the intuitiveness and refinement of inverse design. A gradient optimization method based on discrete adjoint equations is proposed to achieve the fast solution of the gradient information of target equivalent area distribution relative to design variables and to drive the aerodynamic shape update to the optimal solution. An optimization experiment is carried out based on a self-developed supersonic civil aircraft configuration with engines. The results show that the equivalent area distribution adjoint equation can accurately solve the gradient information. After optimization, the sonic boom level of the aircraft was reduced by 13.2 PLdB, and the drag coefficient was reduced by 60.75 counts. Moreover, the equivalent area distribution adjoint optimization method has outstanding advantages, such as high sensitivity and fast convergence speed, and can take both the low sonic boom and the low drag force of the aircraft into account, providing a powerful tool for the comprehensive optimization design of supersonic civil aircraft by considering sonic boom and aerodynamic force.