Localized propagation delay signals associated with line-aligned convective cells were detected by the Synthetic Aperture Radar Interferometry (InSAR) technique on 25 August 2010 in Niigata prefecture. The maximum amplitude of the signal reached up to 22.5 cm, which was approximately equivalent to 29 mm anomaly in precipitable water vapor (PWV). The nationwide radar rainfall intensity captured the spatial distribution of hydrometeors on both land and sea, which was similar to that of the InSAR-derived water vapor field, suggesting that the convective cells were initiated on the Japan Sea to the west-southwest of the observation area. A numerical weather model (NWM) simulation with the grid spacing of 2.5 km reproduced line-aligned convective cells with 3 cm smaller maximum amplitude to that in InSAR. A NWM simulation that assimilates Global Navigation Satellite System (GNSS)-derived PWV data for four-dimensional variational assimilation enhanced the water vapor flux convergence at the surface, which improved the amplitude of the localized delay signals. The advantage of the unique water vapor observation by InSAR enabled us to assess the meso-gamma scale NWM reproducibility in terms of water vapor, which is one of the fundamental prognostic parameter for NWMs.