Background: China has great student participation in STEM education. Chinese society has a progressive and positive attitude towards STEM as it is considered to provide more opportunities in life. Teachers play a vital role in the success of any STEM program in K-12 schools. However, teachers are facing instructional challenges because of the interdisciplinary nature of the STEM curriculum and the current typical school structure. The success of the STEM programs depends on teachers' beliefs and their knowledge in adapting to instructional implementation of STEM concepts. Results: The data (n = 216) was collected from STEM primary and secondary teachers from 25 provinces in mainland China. Exploratory factor analysis (EFA) was applied, and Pearson's correlation analysis was used to examine the correlation between Chinese STEM teachers' beliefs, knowledge, implementation, and the intrinsic challenges of STEM education; "t" tests and analysis of variance (ANOVA) were performed to ascertain whether there were differences. The structural equation model (SEM) was applied to identify interrelationships. The results indicated that Chinese STEM teachers encounter higher-level intrinsic challenges to instructional implementations based on their beliefs and knowledge. Teachers who utilize their experience of teaching science as their main discipline and then attempt to integrate STEM using mathematics and engineering are likely to encounter higher-level intrinsic challenges in implementation. Conclusion: The intrinsic challenges perceived by Chinese teachers in the practice of STEM education can be predicted by their beliefs and knowledge base. Teachers who understand the nature and pedagogy of STEM education are more likely to encounter lower-level intrinsic challenges of STEM teaching, while teachers who utilize their main discipline when conducting integrated STEM learning activities through modeling based on science, technology, engineering, and mathematical problem situations are more likely to encounter higher-level intrinsic challenges. This study also reveals that there are some significant differences in the level of STEM teachers' beliefs, knowledge base, instructional practice, and their intrinsic challenges based on their teaching grade, seniority, and experience of STEM training and teaching.