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!