Based on the welding characteristics of laser deep penetration welding, a three-dimensional transient thermal-flow coupling model of laser welding was established in the process when filler was melted into molten pool. The effect of filler metal filling mode on the three-dimensional shape of keyhole and the flow behavior of molten pool was studied. Finally, the influence mechanism of filler metal filling on keyhole stability was analyzed. The results show that filler metal in the form of a free transition into the molten pool had larger impact on the keyhole shape, causing the keyhole to close and collapse. The filler metal in the form of filling along the edge of the molten pool into the molten pool had relatively small impact on the keyhole shape, the keyhole bottom appeared concave phenomenon. After filler metal filled into the molten pool, two clockwise flow vortices were produced behind the keyhole wall, which made the flow behavior of the molten pool more complex.