Counterpart is the right word, as shown with Barrie's research in the OED:
A person or thing not exactly similar to another, but serving as its equivalent in a different context.
There is a question about number, though.
Each branch is treated as singular, or at least considered individually, and if there is only one marketing manager in each branch, your sentence should be
He knows his counterpart in each branch.
An equivalent when considering plural branches, and therefore more than one manager, is
He knows his counterparts in other branches.
If there is more than manager per branch, then counterparts in each branch is fine.