Pair programming (PP) can help improve students’ computational thinking (CT), but the trajectory of CT skills and the differences between high-scoring and low-scoring students in PP are unknown and need further exploration. In this study, a total of 32 fifth graders worked on Scratch tasks in 16 pairs. The group discourse of three learning topics (comprising 9 projects) was collected. After the audio files were transcribed, 1,303 conversations were obtained. They were analyzed via Epistemic Network Analysis (ENA) Webkit, which can reveal the trajectory of students’ CT development via analyzing codes of discourse related to CT in PP. Three Scratch learning topics were assessed based on the Dr. Scratch platform to acquire the level of students’ CT and to determine the low- and high-scoring groups. Results indicated that CT concepts and CT practices were always closely related in PP and CT practices, and CT perspectives could be gradually and closely related after a long period of CT training. A significant difference between the two groups’ CT structures was found. The high-scoring group had more fragments of CT practice and connecting of CT perspectives, while the low-scoring group showed more fragments of CT concepts and expressing of CT perspectives. This research provides insights into cultivating primary school students’ CT using Scratch in the context of PP. The findings can provide suggestions for instructors to design instructional interventions to facilitate students’ CT skills via PP learning. Instructors can improve CT skills by guiding students to constantly ask questions, and specifying the role swap between driver and navigator in PP. Besides, instructors could give more consideration to the development of CT perspectives, and especially the ability to question.