Abstract: In the face of a new round of global sci-tech revolution and industrial transformation, traditional liberal arts education is unable to meet the demand for interdisciplinary and innovative talents in the era of digital economy. And the construction of new liberal arts with typical characteristics of interdisciplinary integration rises to the occasion. Innovation and entrepreneurship education is the key field in cultivating talents in new liberal arts. Their objectives are consistent, and their operational structures are compatible. Therefore, integrating innovation and entrepreneurship education reform into the construction of new liberal arts is the only way to improve the quality of higher education in China. The study finds that current innovation and entrepreneurship education in colleges and universities has not been effectively integrated into the new liberal arts education, and there are still some deficiencies in top-level design, curriculum system, teaching staff, cultivation mode, and so on. In view of this, this paper first expounds the concrete measures for building the innovation and entrepreneurship education system of the new liberal arts in universities with advantages in engineering. It then puts forward three core elements for the construction of the innovation and entrepreneurship education system: support system, curriculum system, and evaluation system. In addition, taking Beihang University as an example, this paper summarizes the beneficial experience of the universities with engineering advantages in order to provide reference for the construction of the innovation and entrepreneurship education system for liberal arts and management majors in universities of science and engineering.