Page 180 (section 7.4.1) of CLRS 3rd edition says
a worst-case split at every level of recursion in quicksort produces a $\Theta(n^2)$ running time
It seems that $\Theta(n^2)$ should be $\Theta(n)$ since lines 5~6 of the PARTITION procedure run n times at most.
Is my understanding correct?

The original statement starts with "we saw in section 7.2". Section 7.2 contains the following, which explains the statement above in detail.
Basically, as you have observed, any partitioning of an $m$-element (sub)array costs $\Theta(m)$ time, with any split, whether in worst-case or not. With "a worst-case split at every level of recursion", the quicksort partitions an array of $n$ elements, then a subarray of $n-1$ elements, then a subarray of $n-2$ elements, and so on until a subarray of 1 element at last. If we sum the costs incurred at every level of the recursion, we see the total running time is $\Theta(n^2)$.
Put in another way, "a worst-case split at every level" means "worst-case splits at all levels".
It is a standard convention to describe "all" items by "every" item.
"A worst-case split at every level of recursion in quicksort" here should be understood as "Running quicksort that splits at every level of recursion in the worst way", instead of "Running one level of recursion in quicksort" with "a worst-case split".
For quicksort that runs with a worst-case split at every level of recursion,
The $k$-th level runs in $\Theta(n-k+1)$ time.