Questioning is a critical instructional strategy for teachers to support students' knowledge construction in inquiry-oriented science teaching. Existing literature has delineated the characteristics and functions of effective questioning strategies. However, attention has been primarily cast on the format of questioning like open-ended questions in prompting student interactions or class discourses, but not much on science content embedded in questions and how they guide students toward learning objectives. Insufficient attention has been cast on the connection between a chain of questions used by a teacher in the attempt to scaffold student conceptual understanding, especially when students encounter difficulties. Furthermore, existing methods of question analysis from massive information of class discourses are unwieldy for large-scale analysis. Science teacher education needs an instrument to assess a large sample of Pre-service Teachers' (PST) competencies of not only asking open-ended questions to solicit students' thoughts but also analyzing the information collected from students' responses and determining the logical of consecutive responses. This study presented such an instrument for analyzing patterns of 60 PST's questioning chains from when they taught a science lesson during a methods course and another lesson during student teaching. Cohen's Kappa was conducted to examine the inter-rater reliability of the coders. The PST's orientations from the two videos were determined and the correlation between them was compared to test the validity of this instrument. Consideration of the data from this instrument identified patterns of the PSTs' science teaching, discussed the importance of guiding questions in inquiry teaching, and suggested quantitative studies with this instrument.