This paper aims to develop the IDL-C system to cultivate the professional core literacy of science education teacher trainees through deep learning technology and science education theory. The authors constructed a model for assessing the effectiveness of core literacy development containing multiple algorithms to determine the system’s effectiveness. They conducted an empirical study using the example of Science Education College in S city. The values of teacher trainees in clustering as good and excellent are relatively close to each other, 0.4480 and 0.4246 respectively, and their cultivation effect is approaching from good to excellent, and the total score of the measurement = 0.685 × “Civic and Political Literacy” + 0.411 × “Foundation Literacy” + 0.091 × “Practical Literacy” + 0.111 × “Innovative Literacy”, which is most related to the cultivation of Civic and Political Literacy. The study not only enhances the core literacy of science education teacher trainees, but also promotes the modernization and reform of science education.