Я знаю Москву, большой город.
Я знаю, Москва - большой город.
Both these sentences are correct. But in the first sentence the main clause is "Я знаю Москву", in the second one the main clause is "Москва - большой город."
"большой город" in the first sentence is some clarification, it's not the main fact that you tell and if you extend that sentence to "Я знаю Москву, большой город, 10 лет", the main fact will be "Я знаю Москву 10 лет".
For example "Я знаю Урал, большую реку". "Урал" has many senses. The addition "большую реку" explains that it's not about the region or something else. If one say "Я знаю, Урал - большая река" they confirm the fact that Урал is a big river.