<p>Elucidating the underlying mechanisms of negative thermal expansion (NTE) and structure flexibility is crucially important for basic research and industrial technology. While chemical modification can enhance the versatility of NTE materials, it also typically leads to a significant reduction in their thermal expansion coefficients, making the understanding of these underlying mechanisms both important and full of challenges. Here, a notable phenomenon was observed where partial Mn substitution enhances NTE coefficient of Zn₂GeO₄ system. A joint study of high-resolution synchrotron X-ray diffraction, Raman spectra, and density functional theory calculations was conducted to elucidate the correlations between its crystal structure and thermal expansion, as well as the mechanism behind. Mn doping was found to enlarge the lattice parameters and increase the asymmetry of O atoms, thereby enhancing the structural flexibility of Zn_2−<i>x</i>Mn_<i>x</i>GeO₄. This improved flexibility facilitates enhanced transversal thermal vibrations of O atoms. Notably, the Grüneisen parameters of low-frequency phonons of Zn₂GeO₄ become significantly more negative upon Mn doping, giving rise to the enhancement of NTE properties. This work not only reveals the mechanism of structural flexibility and NTE in Zn_2−<i>x</i>Mn_<i>x</i>GeO₄, but also provides valuable references for tailoring the coefficients of thermal expansion in other open-framework structure materials.</p> Graphical abstract <p></p>