The invention provides an automatic control system and an automatic control method for ship heeling balance. Multiple anti-heeling pumps capable of independently working and multiple pairs of anti-heeling ballast tanks are arranged in the automatic control system, so that rolling of a ship in a moored condition, at various navigational speeds, such as a medium-high navigational speed, a low navigational speed and a zero navigational speed and under various encounter wave directions can be effectively reduced, and heeling and trimming caused to the ship by various factors: loading unbalance, local cabin breakage and wind pressure, are rapidly compensated, so that special engineering ships like pipe-laying ships and the like have low economic risk, can adapt to severe environment conditions, and meanwhile, have the characteristics of operational safety of offshore working, and the like. The automatic control system and the automatic control method for the ship heeling balance have very good popularization and use value.