The design of the illumination pattern is crucial for improving imaging quality of ghost imaging (GI). The S-matrix is an ideal binary matrix for use in GI with non-visible light and other particles since there are no uniformly configurable beam-shaping modulators in these GI regimes. However, unlike widely researched GI with visible light, there is relatively little research on the sampling rate and noise resistance of compressed GI based on the S-matrix. In this paper, we investigate the performance of compressed GI using the S-matrix as the illumination pattern (SCSGI) and propose a post-processing method called preconditioned S-matrix compressed GI (PSCSGI) to improve the imaging quality and data efficiency of SCSGI. Simulation and experimental results demonstrate that compared with SCSGI, PSCSGI can improve imaging quality in noisy conditions while utilizing only half the amount of data used in SCSGI. Furthermore, better reconstructed results can be obtained even when the sampling rate is as low as 5%. The proposed PSCSGI method is expected to advance the application of binary masks based on the S-matrix in GI.