Is that possible to host several phabricators in one single server?

Why do you want completely separate installations? From your description, it sounds like you want Spaces instead. Spaces allows you to namespace different parts of Phabricator such that things within the Engineering namespace wouldn't necessarily be accessible to the HR namespace.

The main reason is that we did a lot of customizations on maniphest, and makes the maniphest impossible for HRs to work with.

e.g. this is one of our maniphests:

HRs need a completely different set of fields.

Or did I miss anything here? Is that possible phabricator support different manipheste fields config in different spaces?

No, that's not currently possible, but it might be worth filing a Maniphest task for that.