By utilizing the relationship of different baselines, the multi-baseline interferometric synthetic aperture radar (InSAR) can significantly enhance the capability of obtaining higher accuracy of the elevation measurement than that of traditional single-baseline InSAR. A novel filtering method of multi-baseline InSAR interferogram based on signal subspace processing is presented here. In the novel filtering method, we regard each pixel unit of different interferograms of different baselines as a training sample. Then the filter based on subspace tracking operation can effectively filtrate the noise interference of all the interferograms. Monte Carlo tests and simulated InSAR data validate that the new approach can achieve better filtering effect with similar levels of the execution time than the pivoting average-filter and the pivoting median-filter.