how I can add a cooldown to this tool animation?

You can add another wait() function AFTER check if statements

There's not much to explain but if you want to add a cooldown to the tool then you can use the wait() function. This is THE most simple way of adding a cooldown because there's only 1 code line. I also fixed some of the code

Tool.Activated:Connect(function()
   local humanoid = script.Parent.Parent:WaitForChild("Humanoid")
   if Enable == true then
      Enable = false
      if Check == 0 then
         humanoid:LoadAnimation(script.Anim03):Play()
        script.Parent.Combo.C0:FireServer(script.Parent.Handle.HitPart)
        script.Swing:Play()
        wait(0.6)
        Check = 1
      else if Check == 1 then
        humanoid:LoadAnimation(script.Anim04):Play()
        script.Parent.Combo.C1:FireServer(script.Parent.Handle.HitPart)
        script.Swing:Play()
        wait(0.6)
        Check = 0
      end

      wait(5) -- Add 5 seconds cooldown
      Enable = true -- Move enable to this line because it's better

    end
end)

In the future, you probably want to know many methods which can delay things such as the wait() function which is the simplest in delaying things.

Happy Scripting!