The aerodynamic design of supersonic aircraft necessitates the comprehensive consideration of multiple conflicting design objectives and multi-disciplinary characteristics. However, the efficiency of heuristic algorithms in solving multi-objective aerodynamic problems significantly decreases with the increase in the number of design variables and objectives. Although gradient-based adjoint optimization methods can eliminate the constraints of design variables on aerodynamic optimization and have high optimization efficiency, they are prone to getting stuck in local optima and are difficult to apply in multi-objective optimization. To overcome these shortcomings, a manifold-guided multi-objective gradient-based algorithm (MG-MOGBA) is proposed. This algorithm enhances the optimization efficiency of the algorithm by coupling the multi-objective gradient operator with the predicted Pareto front (PF) manifold structure to guide the population search direction and reduce the search space. A multi-objective aerodynamic optimization framework based on the discrete adjoint method is developed to automate the aerodynamic optimization process. Test functions and airfoil optimization results confirm that the proposed algorithm achieves superior results with fewer iterations and is more efficient than heuristic algorithms. The four-objective supersonic civil aircraft example demonstrates that the algorithm can effectively handle high-dimensional multi-objective aerodynamic optimization problems. A potential equilibrium solution increased the cruise factor by 17.5% and 12.8% under supersonic and transonic conditions respectively, reduced the maximum overpressure of the sonic boom by 25.1%, and decreased the root bending moment by 20.3%. Overall, MG-MOGBA can efficiently solve high-dimensional multi-objective aerodynamic optimization problems and has good scalability for the dimensions of design objectives and variables.