A non-deity Cleric (Nature Domain) can solve your problem
I do that in my Salt Marsh campaign - which is ostensibly set in the World of Greyhawk. What I have chosen to do as DM is use the Forces and Philosophies approach. You can find a summary of that in the DMG, pages 10-13.
You will also find mentions of "Nature" as a power source in the class write up for the Druid class
p.64 PHB (Power of Nature)
Druids revere nature above all, getting their spells and other magical
powers either from the force of nature itself or from a nature deity.
The "divine forces of nature" is referred to in the descriptions, in Chapter 10, of how The Weave is accessed by various spell casters.
All magic depends on the Weave, though different kinds of magic access
it in a variety of ways. The spells of wizards, warlocks, sorcerers,
and bards are commonly called arcane magic. These spells rely on an
understanding - learned or intuitive - of the workings of the Weave.
{snip} The spells of clerics, druids, paladins and rangers are called
divine magic. The spell casters' access to the Weave is mediated by a
divine power - gods, the divine forces of nature, or the sacred weight
of a paladin's oath. (p. 205 PHB)
"Nature" need not be personified by your setting deity any more than "The Tempest" needs to be personified as Umberlee in the Forgotten Realms. If your player wants to be a Nature domain cleric and your nature deity is a bad fit, "Nature" itself can be the source of their divine power.
And maybe this cleric will, over the course of your campaign, set up a few shrines and springs where Nature is worshipped or revered. Play and find out.
But what if he wants another deity?
You mentioned in a comment "I'm pretty sure he wants do use a deity"
You, as the DM, have two choices here.
- Simply say "no" since you are the world builder.
(PHB, p 6) Ultimately, the Dungeon Master is the authority on the
campaign and its setting, even if the setting is a published world.
- He has to invent the deity, write it up in detail, and provide it to you for final approval. I did this in my brother's campaign, he approved it with just a few tweaks, and we now have an added deity in the campaign named Stahnuld: the god of beer, wine and whisky.
An added advantage of using option 2 is that it likely adds to the "buy-in" that this player has for your game world.
Opportunities abound
You mentioned in a comment this about your setting's nature deity:
There is a nature god, but it's currently sorta dead/ doesn't have
religions worshipping it.
This has the potential to turn into a great character arc for this PC to develop over the course of the campaign. Perhaps, over time, the PC slowly reinvigorates the worship of that deity and revives interest in it. Or, per your other comment,
By not worshipped, I mean all non fae species dislike that deity due
to causing a genocide/ massive problems to the modern day.
Your PC's cleric can lead the way in establishing a new Nature based faith, which could in time result in a new deity arising or being recognized and revered. This PC can make an impact on the game world, which in turn can augment your own world building. While that will depend on how long the campaigns lasts, and how your player responds, there are some great opportunities for something new to grow organically over the course of their adventures.