It is a new direction and requirement of higher engineering education to strengthen the cultivation of innovative talents and reform of teaching mode under the background of emerging engineering education. According to the shortcomings of the evaluation system of students' innovation ability in traditional teaching practice, this paper reforms the evaluation method of innovation ability with the research background of the cultivation of innovative talents in transportation and civil engineering. Based on the three aspects of whole process, multi-subject and multi-dimension, highlighting the cultivation process of innovation ability, multi-dimensional optimization of innovation practice activities, taking into account the common development of teachers and students, sticking to the cultivation quality standard, the multi-subject multi-dimensional efficiency evaluation method centering on the whole process of innovation ability promotion and cultivation is constructed. Good results have been achieved through practical application, which can provide reference for civil engineering major and related colleges to innovate talent training mode.