The special holiness of Jerusalem stems from its being “the site that God will choose,” the city where God decided to establish His House, the Temple, so that His Presence should dwell there.
This connection between God and the city of Jerusalem is found not just in Heavenly Jerusalem, in the spiritual part of the city, but also in earthly Jerusalem, the city as we know it.
This may be compared to a geological fault.
When the earth, which is composed of strata, is fractured as a result of various pressures, one section is displaced and pushed upward in relation to other sections, whereupon it can be seen that the strata are no longer continuous.
Upper strata lie next to strata that formerly were much deeper.
Similarly, in Jerusalem, instead of the upper and lower worlds being in normal relation, one above the other, they meet.
Instead of the heavens being above and the earth below, there is a point at which heaven and earth are on the same plane.
The contact between heaven and earth is expressed in its most radical form in the Temple’s holiest place – the Holy of Holies. The Holy of Holies, as described by our sages, is unlike any other space known to man.
–Rabbi Adin Steinsaltz