Big data is the product of information explosion and accumulation to a degree that leads to change, and it is the result of quantitative change leading to qualitative change. Individuals are both consumers and producers of data on the Internet. The era of big data for large-scale production, sharing and application of data has come. The public health curriculum system is an important curriculum, which aims to cultivate students' healthy thinking mode. In order to exert the synergistic effect of ideological and political education, it is necessary to integrate ideological and political education into the public health curriculum system. This paper introduces the public health system in the new era. Taking a medical college student as the research object, using the methods of questionnaire survey and data analysis, this paper applies the UMU platform to carry out the teaching and evaluation of online courses, studies the comprehensive evaluation of the public health system driven by big data with actual cases, and finally puts forward the integration countermeasures of the college ideological and political work and public health curriculum system in the big data era. The results show that online courses can reduce students' test anxiety (P<0.01), improve their cognitive strategies (P<0.01), and the application of UMU platform can facilitate students' learning, improve their self-learning ability, and achieve good teaching results. Moreover, based on big data analysis technology, online courses can be introduced into the evaluation of ideological and political education effects, which not only realizes the overall evaluation, but also realizes the presentation of individual situation effects, And in the process of education, the deviation can be corrected to improve the effect of ideological and political education.