The present invention relates to the technical field of automatic packaging, in particular to an automatic packaging system for live fish, comprising a first platform, a second platform and a third platform, the first platform, the second platform and the third platform are arranged in steps, and The first platform is higher than the second platform, and the second platform is higher than the third platform. There is a holding pool on the first platform, the bottom of the holding pool is connected to one end of the waterway, and the other end of the waterway is lower The invention also discloses an automatic packing method for live fish at the bottom of the holding pond, which includes the following steps: S1, opening the water channel; S2, catching fish; S3, weighing; S4, packing and transporting. The invention changes the layout design of the whole packaging system, reduces work intensity and fatigue, reduces the setting of the climbing transmission mechanism, and saves manpower and material resources.