Methodological discussions in the fields of humanities are among the most important effective factors in development of humanities especially Quranic studies. This issue will help the researcher to have a better understanding of the process of religious studies as well as the background formed to the religious texts. Accordingly, by developing new methods, it will be possible to discover and extract the deep semantic layers of the verses of the Holy Quran. Applying descriptive methodology and qualitative and quantitative content analysis, the paper deals with the study of Tafsir Al-Mizan and describes its methodology. Selecting Surah Al-Qafir, the study has investigated Allameh Tabatabaie’s methodology along with taking each commentary proposition of this methodology into account. Finally, Allameh’s methodology in Surah Al-Qafir has been analyzed through quantitative data, tables, and statistical diagrams by using SPSS software. The results of the study suggest that Allameh has interpreted the verses of surah Al-Qafir by enjoying rational interpretation method more than other methods and the most statistics of quantitative analysis are related to this area.