In order to increase the message volume in limited bandwidth for new generation BDS（BeiDou navigation satellite system） RDSS(radio determination satellite service), the signal was modulated on multi-subcarriers inferring to orthogonal frequency division multiplexing. Modulation on multi-subcarriers was rarely used in navigation systems. Corresponding analysis mainly focuses on multiple access affection, and loss caused by carrier frequency offset and code phase offset were analyzed separately. It is not considered that when using the same synchronization head, the signals on other subcarriers can cause high correlation peak for the observed subcarrier. This may affect the receiving of signals. The mechanism is analyzed and two correlation mitigation methods are supplied, which offers certain guidance for the design of the follow-up system.