In many countries, integrating engineering into science education is regarded as the best means of improving science, technology, engineering, and mathematics (STEM) education. In Mainland China, some efforts have been made to integrate engineering into science, but problems regarding teacher factors hinder its effective implementation. To address these problems, we conducted a survey together with classroom observations and interviews to explore science teachers' perceptions of the integration of engineering into science (IEIS) with aims of exposing the problems and the status of IEIS implementation. The study involved 1185 science teachers from junior secondary schools in Shanghai. Ten teachers were interviewed, and 5 teachers' classrooms were observed. The findings of mixed research methods revealed the science teachers generally established good understanding of engineering and engineering education; however, the problems are: (1) science teachers failed to identify engineering practices and scientific practices; (2) they designed and implemented IEIS in low integration levels with low cognition level of engineering education; and (3) there was a lack of high-quality IEIS training programme for STEM education. The results of this study will inform science teacher education and STEM implementation.