To accurately predict the aerodynamic and thrust characteristics of supersonic cruise missile during flight, an integrated online identification method for aerodynamic and thrust parameters was proposed. Motion model of supersonic cruise missile powered by a solid rocket ramjet engine in the longitudinal plane was established, and a polynomial model of aerodynamic and thrust coefficients in the cruise phase was established. The unscented Kalman filtering method was used to conduct online identification and simulation verification of aerodynamic and thrust parameters. The identification performance was compared and verified based on flight test data. Research had shown that the integrated identification of aerodynamic and thrust parameters for supersonic cruise missile was necessary and effective, and the proposed method can be applied to online parameter identification during flight.