Due to the vulnerability of GNSS signals, anti-interference is always an important issue in many GNSS applications. The Frequency domain interference suppressor (FDIS) is an effective approach to suppress CW, swept frequency and narrowband interference for the BPSK signal receiver. However, it is problematic to apply the FDIS directly in the BOC signal receiver. The main problem is that the frequency bandwidth of the BOC signal need to be processed with FDIS is much larger than that of the BPSK signal. It is well known that the spectrum of BOC signal is spilt, and the energy allocated between the upper and lower sidebands is very little. This indicates that a great amount of frequency bins are actually wasted by the useless frequency band between the upper and lower sidebands of the BOC signal. Since the Dual BPSK Tracking (DBT) method explicitly utilizes the split spectrum characteristics of BOC signals, we proposed an improved FDIS for the high order BOC signal receiver by combining both FDIS and DBT methods. Specifically, two finite impulse response (FIR) filters with the same group delay are added after the mixers in the receiver firstly to isolate the upper and lower sidebands of the BOC signal. Then two FDISs are applied to the upper and lower sideband digital signals after down sampling, respectively. Finally, the output signals of FDIS are transferred to the DBT architecture for signal acquisition and tracking. Both the theoretical and the simulation experiments verified that the proposed method could suppress interference effectively and obtain high-precision ranging results.