Abstract: Spectrum of shortwave channels becomes less and less,narrow-band interference has such high density that signal-to-noise ratio of received signal worsen badly in the wideband shortwave probe system. The traditional interference rejection algorithm based on subspace tracking brings high distortion of the probe signal, which results in disadvantageous influence to the high accuracy estimation of channel parameters. This paper presents a novel interference suppression algorithm called mark of two-subspace spectrum based on adaptive subspace tracking which not only realizes interference rejection but also effectively reduces distortion of the probe signal. Spectrum of the base-band probe signal is symmetrical, so this algorithm can get the probe signal in the band of interference using mark of interference-subspace spectrum; and separates the band of NBI from the signal effectively via mark of signal-subspace spectrum. The simulation and data processing of our probe system both demonstrate that the new algorithm can keep the original status of the received signal and obtain higher signal-to-noise ratio of correlation compared to traditional algorithm, which can consumedly increase the acquisition probability of received signal. So our new algorithm called mark of two-subspace spectrum has special important meaning to the high accuracy estimation of the shortwave ionosphere parameter.