There are several established approaches to TafsÊr- interpretation of the holy Qur´Én. Al-TafsÊr al-‘IlmÊ - the scientific interpretation of the Holy Qur´Én is one of the approaches which is lately emerged in the discipline of TafsÊr. Tantawi Jawhari and Zaghloul Naggar are two prominent Egyptian Muslim scholars who focused on scientific issues of the Qur´Én in their tafsÊr works “Al-JawÉhir fÊ tafsÊr al-Qur´Én al-karÊm and “TafsÊr al-AyÉt al-Kawniyyah” respectively. They interpreted the Qur´Énic verses from scientific viewpoint. They agreed on some issues while differed on some others. In this connection, this paper aims to clarify the methodology of both scholars in their TafsÊr using a comparative analysis method. Among the most significant findings of this paper is that the interpretation of Zaghloul Naggar are more precise as well as relevant to the applied science compared to the interpretation of Tantawi Jawhari. This paper also concluded that proper Qur´Énic knowledge and scientific insights are required for the one who wants to interpret the Qur’anic verses concerning the natural phenomena and the scientific indications; otherwise, lacking in any of them will lead to misinterpretation of the message of Allah- the guidance of humankind.