The “General High School Geography Curriculum Standards (2017 Edition, 2020 Revision)” states that the middle school geography curriculum is a fundamental subject course that encompasses both compulsory education geography and high school geography courses. Its content reflects the essence of geography and embodies the basic ideas and methods of geography. Instructional design is a crucial link in cultivating and implementing students’ core competencies. In previous research on middle school geography instructional design, we have placed more emphasis on the micro-level study of specific teaching content and methods guided by core competencies, while less attention has been paid to the relationship between geographical thought and instructional design. Therefore, this article will position geographical thought in middle school geography instructional design from a macro perspective and explore the relationship between the two. To better leverage the unique educational value of geography, it is imperative to infuse geographical thought into middle school geography teaching, adhere to the methodological system of geography, and establish a student-centered classroom teaching model aimed at cultivating core competencies in geography, thereby laying the foundation for students’ lifelong development.