What does it mean to be under the jurisdiction of the pentagon? It's an office building. What jurisdiction does it have?

Saying the Pentagon is an office building is like saying the White House is a single family home.

In fact, the Pentagon and the DoD are synonyms in most usage.

Which doesn't make a lot of sense in the context of the original sentence.

Anything under DoD should be considered military, as it falls under the jurisdiction of the DoD, which is military.

A little circular.

It is a building where the DoD and all of the top military brass work. All DoD aka "military" decisions ultimately come from the Pentagon, where the final say for all things DoD reside.

Disclaimer: I never worked at the pentagon, but am a US Army veteran who was in Military Intelligence from 2001-2005.

Metonymy