ABSTRACT Scientific explanation has been widely recognised as one of the primary proficiencies in global science education. From research and practical perspectives, investigating the cognitive process of constructing scientific explanations by integrating core ideas is essential to make sense of phenomena or solve problems. This study applied the cognitive diagnosis modeling (CDM) approach to diagnose students’ cognitive patterns of constructing scientific explanations by integrating chemical reactions and patterns. We localised three well-designed assessment tasks and correspondingly developed five cognitive attributes. Responses from 244 Grade 9 students in two middle schools were collected, scored, and analyzed. Results show that the five developed cognitive attributes are reliable and effective in identifying students’ cognitive challenges in constructing scientific explanations in a content-specific domain. In addition, we articulated students’ potential cognitive process of constructing scientific explanations. We identified a primary cognitive pathway that students may follow: making correct claims, finding sufficient evidence based on data patterns, and providing scientific principles for the reasoning process. The cognitive diagnosis results could be used to guide teachers in selecting teaching materials and strategies and arranging lesson sequences to support the development of students’ scientific explanations by integrating chemical reactions and patterns.