A multi-layer semiconductor element package structure with surge protection function includes a substrate unit, an insulated unit, a one-way conduction unit and a protection unit. The substrate unit has at least one top substrate, at least one middle substrate and at least one bottom substrate. The insulated unit has at least one first insulated layer filled between the top substrate and the middle substrate and at least one second insulated layer filled between the middle substrate and the bottom substrate. The one-way conduction unit has a plurality of one-way conduction elements electrically disposed between the top substrate and the middle substrate and enclosed by the first insulated layer. The protection unit has at least one protection element with anti surge current or anti surge voltage function electrically disposed between the middle substrate and the bottom substrate and enclosed by the second insulated layer.