This study used the Pathfinder Network to assess student knowledge structure of astronomy learning. The subjects included four teachers, 23 high achievement sixth-graders, and 22 low achievement sixth-graders in natural science. All participants judged the relatedness of nine of the important concepts in astronomy learning. Network representations of the rating data were derived using the Pathfinder scaling algorithm. The similarity between each student’s and the teachers’ networks was then assessed using PRX, GTD, and PFC. The main findings were as follows:(1)The knowledge structures of students with high natural science achievement were closer to the teachers referent structure than those of the students with low achievement. (2)The student-teacher similarity had no significant difference by student’s gender comparison. (3)The PRX index was the most predictive of students’ natural science score among the three indices.