Given the Universe is the set of natural numbers, then $(∀x)(∃y)(x>y)$ is false. But then why is $(∀x)(∃y)(x\geq y)$ true?
The first equation and the second equation is the same except for "=" in the second equation. so i don't get how that affects the statement to this degree. Thank you.
Look at the smallest number in the natural numbers $\mathbb N$ (since you mention that the universe is the set of all natural numbers): the smallest number in $\mathbb N$ would be $0$ or $1$, depending on your definition. Let's just go with $0$.
Since $0 \in \mathbb N$, the universally quantified "x" means the inequality must hold for every natural number $x$, including $x = 0.\;$ Now, does there exist any $y \in \mathbb N$ such that that $0 > y\;$?
On the other hand, if we allow equality too, then we have that it is true that there exists a $\,y \in \mathbb N\,$ such that $\;0 \geq y,\,$ namely, $\,y = 0:$ That is, it is certainly true that $\;0 \geq 0.$
The same logic applies if $x = 1$ instead of $x = 0$, if you are working with a definition of the natural numbers $\{1, 2, 3, \ldots\}$.