The invention relates to the field of submarine exploration, particularly to a submarine rod automatically connecting method and a penetrating rod automatically recovering and separating method. The submarine rod automatically connecting method comprises the following steps of (1) mounting a rod automatically connecting device onto the upper portion of a penetrating device and inside a penetratingmechanical arm and extending a probe or a penetrating rod out of a through hole of a bottom frame; (2) clamping the penetrating rod through a penetrating rod clamp inside a penetrating rod sleeve, sliding the penetrating rod clamp down along a clamp moving track to feed the penetrating rod down to the hole of the bottom frame and fasten the penetrating rod to the tail of a probe/penetrating rod to be connected; (3) through an anchor bolt connector, pushing an anchor bolt inside an anchor bolt box to sequentially penetrate through a hole I and a hole III to fixedly connect the penetrating rodwith the neighboring penetrating rod/probe; (4) through action of a powering mechanism, achieving connection of cables; (5) through operation of a penetrating rod connecting mechanism and the poweringmechanism achieving fixed connection of the penetrating rods and connection of the cables. The submarine rod automatically connecting method achieves multiple connection of the penetrating rods underthe seat as well as automatic connection of penetrating rods of any length of the penetrating device.