To me it seems that your main issue is not having decided a common background-language for your story.
In fantasy novels, either you

Invent a whole new language (cfr. Tolken)
Borrow languages from the real world

Since the Lord of the Rings, a lot of authors have tried the first approach with various degrees of success (keep in mind that Tolkien was a philologist, so he was a little more equipped for the task than your average nowaday writer). With "various degrees of success" I mean that in the worst case, you can tell that the author is just making up words, with little care or sense for phonetic or grammatical coherence.

The second approach is equally viable and doesn't require you to be skilled linguist. You wouldn't be the first to use Latin in a setting were latins didn't exist. Language is a mean to an end: most readers will accept that you are using Latin-esque names to give off an aura of authority. Latin are greek are already used in scientific contexts, so your readers will fall in quickly.

It's not different from your characters talking in English, even if there is no reason for them to do so.

Of course, you're not stuck with latin or greek. If you want there are plenty of other languages to borrow - from arabic to sanskrit.

So, going back to your question:

How do i properly name a fictional species and describe it?

Either:

Invent your own language and use it coherently

or

Borrow from an existing language (and use it coherently)

With coherence here is that you have to take choices and stick with them. The readers will accept, for example, that the book is written in English and that most words will be English words. They will accept a foreign looking language used in a particular context, also. Those will be implicit rules between you and them.

If you start breaking those rules, eyebrows will start to rise. I can give a good example from your issue:

On the other hand, how do i describe them without taking humans as reference?. There are no humans in this world, so the statement "they have a humanoid form" can't apply to them.

Either accept "humanoid" as a term, or replace it with another term. If there are no humans in this world, probably the term "humanoid" could be replaced by whatever is the prominent race with four limbs and an head (Elfoid or Elfish for Elves, Goblinoid for goblins, and so on ...).
But beware that if you ban terms like "human", you should avoid terms like "man" "woman" "mankind" "anthropomorphic" and so on, because they may not have sense anymore in your setting.

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