Scientific research management is an important component of university management and an important guarantee for the sustainable operation of universities. A mature scientific research management system is a sharp tool to promote the discipline construction and comprehensive strength improvement of universities. Therefore, colleges and universities should actively explore new concepts, models, and mechanisms for scientific research management while continuously improving their own educational quality. Based on the analysis of the current situation of university scientific research management in China, it is of great significance to explore effective ways to improve the quality of university scientific research management in the new era. The quality evaluation of higher education scientific research management in entrepreneurship undergraduate colleges is a classical MAGDM problems. Recently, the TODIM and VIKOR method has been used to cope with MAGDM issues. The interval-valued Pythagorean fuzzy sets (IVPFSs) are used as a tool for characterizing uncertain information during the quality evaluation of higher education scientific research management in entrepreneurship undergraduate colleges. In this manuscript, the interval-valued Pythagorean fuzzy TODIM-VIKOR (IVPF-TODIM-VIKOR) method is built to solve the MAGDM under IVPFSs. In the end, a numerical case study for quality evaluation of higher education scientific research management in entrepreneurship undergraduate colleges is given to validate the proposed method.