The National Assessment of Educational Achievement (NAEA) of Korea is the type of large-scale test measuring students’ educational achievement. It has played a crucial role in monitoring the quality of the national curriculum, improving teaching and learning method, and establishing educational policies. The purpose of this study aimed to gain data for improving the national curriculum as well as teaching and learning method through in-depth analysis of the results of the NAEA for the past three years (2010-2012). This study was performed to identify the features of solving the science problems of middle school students according to their proficiency level; Basic, Proficient, and Advanced. This study revealed the significant information regarding the achievement standards or educational contents that students either fully understood or lacked understanding according to their proficiency level as well as the achievement standards that even advanced level students could not perform successfully. Thus, the findings implied how educational contents or achievement standards could be re-arranged by proficiency or school levels. In addition, we identified specific content that needs to be enhanced in order to meet the needs of students appropriately in different proficiency levels.