With the introduction and implementation of core literacy, scientific thinking (ST) has become an essential goal and key dimension of science teaching. At present, there is no agreement on how to cultivate students' ST. This study took 238 sixth grade students from a public primary school in urban China as research sample, built a theoretical model of scientific thinking development based on the theory of the Bronfenbrenner' ecological systems theory, and used multiple data to explore and analyze the impact path of ST development of primary school students using the fuzzy sets of qualitative comparative analysis method (fsQCA). The development of urban primary school students' ST is the result of multiple factors at the level of individual drive, family environment, school teaching, and social resources. The result of data analysis showed that the influence path of ST development of urban primary school students driven by multiple factors includes three paths: parent participation leading, scientific practice leading, and home-school-community integration. We have interpreted the influence mechanism of each path in detail and put forward the enlightenment for science education policy and practice.