Diffusion MRI-driven tractography, a non-invasive technique that reveals how the brain is connected, is widely used in brain lateralization studies. To improve the accuracy of tractography in showing the underlying anatomy of the brain, various tractography filtering methods were applied to reduce false positives. Based on different algorithms, tractography filtering methods are able to identify the fibers most consistent with the original diffusion data while removing fibers that do not align with the original signals, ensuring the tractograms are as biologically accurate as possible. However, the impact of tractography filtering on the lateralization of the brain connectome remains unclear. This study aims to investigate the relationship between fiber filtering and laterality changes in brain structural connectivity. Three typical tracking algorithms were used to construct the raw tractography, and two popular fiber filtering methods(SIFT and SIFT2) were employed to filter the tractography across a range of parameters. Laterality indices were computed for six popular biological features, including four microstructural measures (AD, FA, RD, and T1/T2 ratio) and two structural features (fiber length and connectivity) for each brain region. The results revealed that tractography filtering may cause significant laterality changes in more than 10% of connections, up to 25% for probabilistic tracking, and deterministic tracking exhibited minimal laterality changes compared to probabilistic tracking, experiencing only about 6%. Except for tracking algorithms, different fiber filtering methods, along with the various biological features themselves, displayed more variable patterns of laterality change. In conclusion, this study provides valuable insights into the intricate relationship between fiber filtering and laterality changes in brain structural connectivity. These findings can be used to develop improved tractography filtering methods, ultimately leading to more robust and reliable measurements of brain asymmetry in lateralization studies.