My Animation doesn't damage on touch ? It damages even if the animation is not used...

The reason it's working when the animation is not being used is because the touched function checks if enabled is true. You've set it to true by default, and when the animation is in progress, in theory, disable the touched event.

This should work:

player = game.Players.LocalPlayer

animation = script:WaitForChild("Animation")
animation2 = script:WaitForChild("Animation2")

enabled = false

ra = player.Character:WaitForChild("RightLowerArm")

dmg = script.Damage.Value -- Damage Value

game:GetService("UserInputService").InputBegan:connect(function(input,proc)
    if  input.KeyCode == Enum.KeyCode.Q then
        if not enabled then
            enabled = true

            local animationTrack = player.Character.Humanoid:LoadAnimation(animation)
            animationTrack:Play()
            wait(0.9)
local animation2Track = player.Character.Humanoid:LoadAnimation(animation2)
animation2Track:Play()
wait(1)
            enabled = false
        end
    end
end)

function onTouch(ra)
    local humanoid = ra.Parent:FindFirstChild("Humanoid") -- Finding Humanoid of The Enemy
    if humanoid ~= nil and enabled == true then
        humanoid.Health = humanoid.Health - dmg -- Where the damage won't work.
    end
end
ra.Touched:connect(onTouch)