丘成桐数学科学中心标志以卡拉比-丘流形（Calabi-Yau manifold）的多维图形为元素结合Y字母同构而成。标志围绕中间字母Y将多维图形平面线条化并整体向外扩散，象征着丘成桐数学科学中心面向全球张开怀抱、广纳人才的开放和包容；标志的色彩源自清华大学校色“紫” 搭配蓝色，既蕴含与清华大学的联系，又具有学术的冷静和理智。整个标志造型简洁庄重、寓意明确、识别力强，准确地体现了清华文化和丘成桐数学科学中心学术研究的主题。
The logo of the Yau Mathematical Sciences Center（YMSC）is composed of Letter Y and multidimensional Calabi-Yau manifold graphics. Surrounding Letter Y, the multidimensional Calabi-Yau manifold graphics are two-dimensionalized and expanded outward, embodying internationalization, openness and inclusiveness of YMSC. Purple and blue are the two colors of the Logo, the former originates from the University color of Tsinghua symbolizing their strong connection, the latter matches harmoniously with the former representing the serenity and rationality of academic research. The whole logo is concise, solemn, meaningful and identifiable, accurately reflecting the profound culture of Tsinghua University and the academic research focus of YMSC.