Ultra-fast lasers can realize selective welding of glasses through nonlinear effect and have the advantages of having high welding accuracy, having small heat-affected zone, having high joint strength and not requiring intermediate absorption layer, which provides a new idea for chip packaging. However, this method is limited to the condition of optical contact, which is difficult to use in engineering applications. To solve this problem, an innovative seal welding method by picosecond laser is presented in this paper. In this method, a picosecond laser performs firstly rapid oscillating scan local welding of the two natural overlap glasses with a large contact gap to form a closed area consisting of spot welds. The glass contact gap in the closed area can be reduced to about 1.5 μm through the solidification shrinkage effect of spot welds. Then a good seal weld without plasma ablation, micro-hole, and micro-crack defects can be achieved by picosecond laser in this closed area to realize seal welding of glasses with a large contact gap. The sealing test results show that the seal welding samples can keep good sealing performance for more than one week.