This phrase refers to the idea that the study of Torah should be conducted with a deep sense of reverence and awe towards Hashem. "יראת שמים" (fear of Heaven) implies a conscious awareness of Hashem's presence and a commitment to aligning one's actions and thoughts with His will. When one studies Torah with "יראת שמים," the learning is not just an intellectual exercise but a spiritual practice aimed at deepening one's connection to Hashem and living a life according to His commandments.
In essence, the phrase emphasizes that Torah study should be infused with a sense of purpose and devotion, where the knowledge gained is applied in a way that enhances one's fear of Heaven and adherence to a righteous path.