Constructing a higher education evaluation system with Chinese characteristics is crucial for advancing the modernization of higher education governance and building a strong higher education country. China has accumulated certain experience in the supervision and evaluation of higher education, and has achieved significant results. However, despite the goals set by the 20th CPC National Congress and the new demand for a high-quality higher education system, challenges remain in the supervision and evaluation of higher education, particularly in evaluation standards, classified guidance, system optimization, and digital transformation. To construct the higher education evaluation system with Chinese characteristics, we need to intensify “Chinese characteristics,” comply with China’s unique history, culture and national conditions, seek the bottom logic for the construction of the higher education evaluation system from the perspectives of the value concept, the governance model and the reform methodology, follow the basic principles of value-directing, classified evaluation, problem orientation, integrity plus innovation, and digital transformation, optimize the government’s evaluation, standardize social evaluation, and strengthen the independent evaluation by colleges and universities.