The invention belongs to the field of aircraft engine design, and relates to a design method for comprehensive suppression of infrared and electromagnetic signal features of an aero-engine. The method comprises the following steps: acquiring an infrared signal radiation intensity target value and an electromagnetic signal RCS target value; determining the average temperature T1, meeting the infrared signal radiation intensity target value, of the visible area of the rear cavity of the engine; determining the cooling flow W1 of the visible part of the rear cavity of the engine according to the average temperature T1; determining an engine cooling channel structure and an opening cooling form which meet the temperature reduction requirement; by electromagnetic simulation calculation, determining angle combinations of multiple groups of typical parts of the engine meeting the requirement that the electromagnetic signals are not higher than the RCS target value of the electromagnetic signals; and by iterative optimization, determining the angle combination of the typical parts of the engine with the minimum electromagnetic signal under the condition of engine thrust. According to the invention, the problem of comprehensive suppression of the infrared and electromagnetic signal characteristics of the engine is solved, so that the infrared signals of the engine are lower and the electromagnetic signal characteristics are smaller.