The purpose of this study was primarily to explore high school students' cognitive structures and to identify their learning difficulties on ethanoic acid through the flow map method. The subjects of this study were 30 grade 1 students from Dong Yuan Road Senior High School in Xi'an, China. The interviews were conducted a week after the students had received instruction on ethanoic acid. The interview narratives were then transcribed into flow maps. Analysis of the flow maps showed that there existed a difference between the individual students' cognitive structure on ethanoic acid, higher academic achievers constructed more enriched cognitive structures and had higher scores for cognitive structural variables than lower academic achievers. Furthermore, the results of the correlation analysis of the students' cognitive structure outcomes, academic achievement and the information processing modes revealed that there was a positive correlation between two of them to some extent; in general, the higher academic achievers tended to have higher cognitive structure outcomes and employed high-order information processing modes. Analysis of the content of the flow maps of all the participants indicated that most of the students knew the main facts about ethanoic acid, but the details were not complete, and the misconceptions were mainly related to the molecular constitution and structure of ethanoic acid as well as to the esterification reaction, while the knowledge of the physical properties and the acidity of ethanoic acid seemed to have been mastered relatively well, as for the applications of ethanoic acid, students only mentioned that it can be used as condiment.