This study aimed to develop a comprehensive diagnostic tool for assessing upper-secondary school students' understanding of isomers, expanding upon existing two- and three-tier conceptual diagnostic methods. By incorporating 'Confidence Rating Factor' tiers within the answer and reason sections, a four-tier test was designed and developed. This test was utilized to evaluate students' comprehension of the isomeric conceptual framework and to identify prevalent misconceptions in terms of quantity, complexity, and typicality. The initial phase involved evaluating the reliability and content validity of the developed test before its distribution, resulting in a total of 385 effective test returned for analysis. Data analysis focused on descriptive statistics of students' scores across each tier and dimension, supplemented by unstructured interviews to gain deeper insights. Results indicated a general suboptimal mastery of isomer conceptual understanding among upper secondary school students. Notably, students exhibited higher scores and confidence ratings in the answer tier compared to the reason tier. At both tiers, there was a significant positive correlation between scores and their confidence ratings. Further examination revealed varying levels of proficiency across different content dimensions, with students demonstrating the strongest grasp on the concept of isomers but facing challenges, particularly in 'number judgment and writing'. The study identified eight misconceptions, classified as moderate, serious, and typical across four dimensions, offering valuable insights for teachers. These insights enable teacher to address students' specific learning challenges related to isomers promptly and effectively, ultimately enhancing their understanding and mastery of the subject.