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One of the issues that hinder the students’ learning progress is the inability to construct an epistemological explanation of a scientific phenomenon. Four-tier multiple-choice (hereinafter, 4TMC) instrument and Partial-Credit Model were employed to elaborate on the diagnosis process of the aforementioned problem. This study was to develop and implement the four-tier multiplechoice instrument with Partial-Credit Model to evaluate students’ learning progress in explaining the conceptual change of state of matter. This research applied a development research referring to the test development model by Wilson. The data were obtained through development and validation techniques on 20 4TMC items tested to 427 students. On each item, the study applied diagnostic-summative assessment and certainty response index. The students’ conceptual understanding level was categorized based on the combination of their answer choices; the measurement generated Partial-Credit Model for 1 parameter logistic (IPL) data. Analysis of differences was based on the student level class using Analysis of Variants (One-way ANOVA). This study resulted in 20 valid and reliable 4TMC instruments. The result revealed that the integration of 4TMC test and Partial-Credit Model was effective to be treated as the instrument to measure students’ learning progress. One-way ANOVA test indicated the differences among the students’ competence based on the academic level. On top of that, it was discovered that low-ability students showed slow progress due to the lack of knowledge as well as a misconception in explaining the Concept of Change of State of Matter. All in all, the research regarded that the diagnostic information was necessary for teachers in prospective development of learning strategies and evaluation of science learning.