Can I make this script have a cooldown?

The tick function returns the amount of time since the unix epoch (January 1 1970). Using this information, the fact that time changes steadily, and some simple math, a cooldown can be implemented into your script.

local Player = game.Players.LocalPlayer --// I assume this is a LocalScript, so you can access the player this way.
local mouse = Player:GetMouse() --// It's a good practice to use local variables.
local lastUse = 0;

local function onKeyDown(key) --// And local functions.
	local Key = key:lower()
	if key == "z" and Player.Levelss.Level.Value >= 15 and tick()-lastUse > 10  then --// Check if it's been ten seconds since the last use.
		local x = Instance.new("Part")
		x.BrickColor = BrickColor.new("White")
		x.Material = "Neon"
		x.CanCollide = false
		x.Transparency = 0.6
		x.Size = Vector3.new(10,10,10)
		x.TopSurface = "Smooth"
		x.BottomSurface = "Smooth"
		x.Shape = "Ball"
		local fd = script.fireDamage:clone()
		fd.Parent = x
		local a = Instance.new("Sound")
		a.SoundId = "http://www.roblox.com/asset/?id=260430117"
		a.Parent = x
		a.Volume = 2
		a:play()
		
		
		local y = Instance.new("BodyVelocity")
		y.maxForce = Vector3.new(math.huge ,math.huge ,math.huge)
		y.velocity = Player.Character.Torso.CFrame.lookVector*95
		
		x.CFrame = Player.Character.Torso.CFrame*CFrame.new(0, 0 , -12)
		x.Parent = Workspace
		y.Parent = x    
		game.Debris:AddItem(x, 6)
		
		lastUse = tick(); --// Set the last use to the current time.
	end
end


mouse.KeyDown:connect(onKeyDown)

I'd recommend converting your code to use UserInputService, instead; mouse.KeyDown is deprecated.

Hope this helped.

PS: See how much more readable your code is when it's indented correctly? I urge you to check out these wiki pages about clean code and indenting. Good luck!