When I Made Food Script, It Not Disappear When Eated, How Do I Fix This?

First: a few nitpicks. On line 10, you don't need to be redefining ps every time the tool is activated. You can put that definition on line 3. Use task.wait() instead of wait(). task.wait() is more accurate and favored by ROBLOX.

Your problem occurs on line 14. The tool only is destroyed if the player's hunger is over 100, because of the end statements being put in poorly. This should fix your issue:

Tool = script.Parent
debounce = false
local ps = game:GetService("Players")

Tool.Activated:connect(
    function(mouse)
        local hum = Tool.Parent:FindFirstChild("Humanoid")
        if (hum ~= nil) and not debounce then
            debounce = true
            task.wait(2)
            hum.Health = hum.Health + 15
            local player = ps:GetPlayerFromCharacter(hum.Parent)
            local hunger = player:FindFirstChild("Hunger")
            hunger.Value = hunger.Value + 20
            if hunger.Value >= 100 then
                hunger.Value = 100
            end
        --your issue was here - end wasn't placed correctly.
        task.wait(3)
            Tool:Remove()
        end
    end)

Tool.Equipped:connect(
    function(mouse)
        mouse.Icon = "rbxasset://textures\\GunCursor.png"
end)