Inquiry is one integral part of science learning. Understanding the underlining meaning and the complete procedures of inquiry-based laboratories would be beneficial to student teachers' future work. Therefore, it is necessary for student teachers to perform inquiry-based laboratories and know how to demonstrate them to school students. However, the differences between cookbook-style laboratories and inquiry-based ones may present obstacles for student teachers if most of them were more familiar with the traditional type. This study examined the potential difficulties that student teachers might encounter when conducting inquiry-based chemistry laboratories. Information was gathered through a self-designed questionnaire, interviews, and student teachers' self-reports. Data from the questionnaire were analyzed to gain a preliminary understanding of what challenges the student teachers had met during the inquiry-based laboratory, from their viewpoints. Results from interviews were combined with those from self-reports to investigate how the challenges had impacted the student teachers' perceptions of the difficulty of the inquiry-based laboratory. This study found some challenges encountered by the student teachers in inquiry-based laboratories that were considered difficult, such as presenting research questions. But not all challenges had influences on student teachers' perceptions of the difficulty level of inquiry-based laboratories. A cyclical progression of students' mental states in inquiry-based laboratories is presented to support research about inquiry-based learning.