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The modernized global navigation satellite system (GNSS) provides the open service (OS) signal and authorized service (AS) signal for users. Each service signal includes a data component and a pilot component. All the signal components need to be combined into a composite signal for broadcast. To verify whether the transmitted signal generated by satellite payload can meet the design requirements, the signal in space is collected by high gain antenna, and the signal quality is evaluated. However, the spreading spectrum code sequences of AS signal are unknown. In order to evaluate the signal quality of AS signal, the code sequences of AS signal have to be recovered. The current methods are based on the following assumptions: the expression of the constant envelope composite signal or the power/phase relationship of AS signal is known. Nevertheless, the above assumptions may be not stratified. This paper studies the code sequences estimation method when the expression of the constant envelope composite signal and the power/phase relationship of AS signal are unknown. The proposed method treats the code sequences as the optimized variables. The utility function to obtain the maximum cross-correlation value is exploited. The optimization problem is solved by the binary genetic algorithm. On this basic, the separation method of AS signal component is presented. The correlation function of AS signal is obtained, and the correlation characteristics of AS signal component are evaluated. The performance of the proposed method is verified by the theoretical analysis and numerical simulation. Finally, based on the proposed method, we evaluate the signal quality of Galileo E1 signal collected by a 6m antenna, which shows the effectiveness of the proposed method.