An incorrect concept map may obstruct a student's comprehension when writing summaries if they are unable to grasp key concepts when reading texts. The purpose of this study was to investigate the effects of automatic scaffolding and measurement of three-layer concept maps on improving university students' writing summaries. The automatic three-layer concept maps presented in this study include: (1) the central idea of the title, (2) the main idea of each paragraph, and (3) the supporting ideas in each paragraph. A sample of 107 university students who studied English as a Foreign Language (EFL) was divided into experimental and control groups, comprised of 54 and 53 students respectively. The results of this study indicate that the students of the experimental group made more significant improvement in reading comprehension and summary writing than those of the control group as they were able to identify the main idea from each paragraph and clarify relations among paragraphs after requesting the three-layer concept maps. They then modified their prior knowledge structure by revising the first-draft summaries to final ones. The students' perceptions toward the automatic three-layer concept maps to improve summary writing are also described in this study.