Greenberg's thought involves a dynamic reading of current Jewish history through use of traditional Jewish categories of thought. He has written extensively about the Holocaust and about the historical and religious significance of the State of Israel.

His great teacher in Jewish Thought was Rabbi Joseph B. Soloveitchik. One of his major contributions has been as a teacher, and a whole generation of distinguished scholars, including Rabbi Joseph Telushkin and Michael Berenbaum consider him their mentor.

Greenberg's thought centers on the concept of 'Tikkun Olam' of humanity working as Co- Creator with God in improving the world. Another crucial concept of his thought is that of 'Covenant' and he sees the Jewish people's Covenant with God as enjoining them to set an example for the moral edification of mankind.

Only part of his post-holocaust theology has been published. Greenberg sees the Holocaust as a seminal event in Jewish history, which should be seen as the "breaking of the covenant" between God and the Jewish People. It is also latest stage in God's tzimtzum from the world. The Holocaust drives home the point that the fate of the world is in humanity's hands. If there can be such a strong evil in the world as manifest in the Holocaust, there can also be realized in the world the most incredible good.

Because of his independent thinking Rabbi Greenberg has frequently met with harsh criticism from fellow Orthodox Rabbis. An initial strong supporter of Israeli settlement in Gush Etzion, he later became critical of some aspects of Israeli policy. Greenberg, however, continues to raise financial support for the Bat Ayin yeshiva, the dormitories of which are named for his late son, J.J., and which is operated by his nephew Rabbi Natan Greenberg.