A new robust threshold setting strategy based on the second-order statistics, which is applied to the model of frequency domain interference suppression (IS) in DSSS communication system, is proposed. The predefined scaling factor is derived according to the distribution characteristic of Rayleigh distribution, which the magnitude spectrum of DS received signal obeys approximately. The threshold is calculated by the second-order statistics of the signal magnitude spectrum combined with the first-order statistics. The new algorithm is more constringent with the iteration. Both theoretical analysis and simulations illustrate that, the new method has good suppression effect to the narrowband interference when the jammer to signal ratio (JSR) goes to 50dB and the percentage of signal bandwidth corrupted reaches 40%.