Flipped classroom is an approach that has been increasingly used in K-12 and higher education. Many studies on the flipped classroom have focused on student behaviors, with inadequate attention to student thinking, which is crucial to learning. Meanwhile, prior studies have examined the effects of visualization tools, such as concept map, on improving student learning through in-depth thinking. Another related approach is knowledge graph, which presents a set of entities and their relationships in a graph as well as in a machine language for further processing and reasoning. It has a potential to support collaborative knowledge construction by automatic combination of individual knowledge graphs. To compare the effects of knowledge graph and concept map on student learning in a flipped classroom, we conducted an experimental study in fifth grade class at an elementary school. Students in the experimental group used a knowledge graph tool in the Learning Cell System, while those in the control group used a concept map tool, XMind, to support their learning of ancient Chinese poetry. The results showed that learning with knowledge graph resulted in better performance in the breadth and depth of subject knowledge as reflected in the students' learning products (ie, concept maps or knowledge graphs).