The high-precision and high spatio-temporal resolution settlement time series data generated by integrating Global Navigation Satellite System (GNSS) and Interferometric Synthetic-Aperture Radar (InSAR) data are of great value for the safe operation of high-speed railways. The GNSS monitoring stations and InSAR monitoring area present zonal distribution along the high-speed railways, which causes the spatial matrix of the GNSS and InSAR data fusion model to be an ill-conditioned matrix. The inverse of the ill-conditioned space matrix is unstable, and it is difficult to estimate the optimal parameter value of the fusion model, which leads to low accuracy and large fluctuations in the fusion of GNSS and InSAR data. We propose a spatio-temporal filter fusion (STFF) method to solve the influence of the ill-conditioned space matrix on the fusion of GNSS and InSAR data, which realizes the high-precision fusion of GNSS and InSAR data along the high-speed railway. First, we propose the kriging model of the adaptive spectral correction method to construct the spatial model of GNSS and InSAR data, avoiding the generation of the ill-conditioned space matrix. Second, iterative almost unbiased estimation is used to obtain the weights of GNSS and InSAR data, avoiding the occurrence of negative variance components. The experimental data are fused using STFF, the spatio-temporal Kalman filter (STKF) method, and the spatio-temporal random effect (STRE) fusion method, respectively. The research results show that the comprehensive performance of STFF is significantly better than that of STKF and STRE. In the spatial domain, the root mean square error (RMSE) reduced by 47% and 46% compared with STKF and STRE, respectively, and the structural similarity index increased by 22% and 16% compared with STKF and STRE, respectively. In the time domain, the RMSE reduced by 29% and 34% compared with STKF and STRE, respectively.