The sentence is incorrect, so it's understandable that you don't understand. I'm assuming they mean 'You're fascinating in a low-key kind of way'. If this is the case, low-key is a more informal way to say 'subtle'. In this case, being 'low-key fascinating', means that they are subtly fascinating, or fascinating in a way that's not obvious. 'Kind of way', is just added to the statement to emphasise the 'low-key'. It doesn't really have any meaning on its own. Saying 'You're low-key fascinating', would still mean the same thing.

As it is written the latter part of the sentence is nonsensical. Low-key is an adjective here, meaning that the person referred to by the speaker is fascinating in a manner that is not super flashy. Low-key is meant to describe something that is more subdued and quiet. For example a "low-key gathering" could be used to describe a small get-together with friends where they're just sitting around chatting. Maybe this sentence was meant to be phrased as "You're fascinating in a low-key kind of way" which means exactly the same thing as "You're low-key fascinating". You can think of "kind of way" as meaning "sort of style" or "sort of manner".