It is considered one of the leading institutions of advanced Torah study in the world and with a student body of roughly 480, it is the second largest hesder yeshiva in Israel.

[10] Yeshivat Har Etzion advocates a combination of Torah study and a love of the Jewish people and the Land of Israel.

The Yeshiva's core philosophy is illustrated by two key works by its founding Roshei Yeshiva: Jewish Values in a Changing World by Rav Amital (Hebrew: והארץ נתן לבני אדם) and By His Light: Character and Values in the Service of God by Rav Lichtenstein (Hebrew: באור פניך יהלכון).

Some have argued that the complexity with which the yeshiva's students regard both Jewish and global matters can be seen as a product of the Brisker methodology, emphasizing as it does the compounded and dichotomous nature of many issues and subjects.

[18] The yeshiva's relatively liberal and open worldview is also seen as a product of this Brisker approach, viewing the world as complex, a composite of many different dichotomous principles, whose inherent tension needs to be recognised.

From the yeshiva's conception it was desired that Tanach would have an important role, something uncommon for Yeshivot at the time, [21][22] and the Yeshiva thus pioneered the "Bible Revolution", "מהפכת התנ״ך", a renaissance in the status of and approach to Tanach study in the Religious Zionist (and broader religious) public, led by Yaaqov Medan and Yoel Bin-Nun.

[22][23] This approach emphasises the literal meaning (peshat) of biblical verses, but also takes into account the overall structure of the relevant section, the context and any intertextual references.

It includes a more psychological and literary approach to character and narrative analysis, often known as "תנ"ך בגובה העיניים" ("Tanach at Eye Level"), all the while incorporating the views and ideas of the Midrash and later Rabbinical commentaries.

[26] The Pedagogic Resource Center of the Herzog College supplements the central Torah library, providing audio-visual material for teachers of Judaic studies in Israel and worldwide.

The Israel Koschitzky Virtual Beit Midrash provides yeshiva-style courses and shiurim (lectures) in Torah and Judaism to students of all ages online.