This study examined the scientific knowledge structure of 3th grade students by using Pathfinder. The results indicated the knowledge structure of an expert group is more organized than amid-or low achievement group. In addition, the indexes of PFC, PRX and GTD also revealed that a high achievement group is higher than a mid-or low achievement group. Furthermore, we analyzed student misconceptions about these two topics by using Pfnet. The finding suggested misconceptions of mid-and low achievement groups are greater than with the high achievement group. Therefore, misconception is the main barrier for learning scientific knowledge.