Downsampling is a routine step before applying Interferometric Synthetic Aperture Radar (InSAR) data to earthquake inversion because of the high computational burden. In this study, we make use of the matrix perturbation theory to describe the downsampling process, which is considered as matrix perturbation on inversion equation. First, we derive a formula to quantitatively assess the perturbation on inversion solution caused by data downsampling. Next, we propose an equation-based InSAR data downsampling algorithm to better reduce the perturbation. The experiment with simulated data demonstrates that our new algorithm preserves the most details from full data inversion comparing with previous algorithms. Finally, we use our method to study the slip distribution of the 2008 Mw 6.3 Dangxiong earthquake.