This study reports an adaptive digital learning project, Scientific Concept Construction and Reconstruction (SCCR), and examines its effects on 108 8th grade students' scientific reasoning and conceptual change through mixed methods. A one-group pre-, post-, and retention quasi-experimental design was used in the study. All students received tests for Atomic Achievement, Scientific Reasoning, and Atomic Dependent Reasoning before, 1 week after, and 8 weeks after learning. A total of 18 students, six from each class, were each interviewed for 1 hour before, immediately after, and 2 months after learning. A flow map was used to provide a sequential representation of the flow of students' scientific narrative elicited from the interviews, and to further analyze the level of scientific reasoning and conceptual change. Results show students' concepts of atoms, scientific reasoning, and conceptual change made progress, which is consistent with the interviewing results regarding the level of scientific reasoning and quantity of conceptual change. This study demonstrated that students' conceptual change and scientific reasoning could be improved through the SCCR learning project. Moreover, regression results indicated students' scientific reasoning contributed more to their conceptual change than to the concepts students held immediately after learning. It implies that scientific reasoning was pivotal for conceptual change and prompted students to make associations among new mental sets and existing hierarchical structure-based memory.