The invention provides a large flexible heat treatment automatic production line with protective atmosphere and a process thereof. The heat treatment automatic production line can use a computer integrated control management system to realize automatic loading and unloading of a material taking vehicle, automatic execution of heat treatment process parameters, online monitoring and real-time regulation and control. The heat treatment automatic production line comprises: a set of high-temperature quenching heating unit, which is composed of three high-temperature quenching heating furnaces; a tempering heating unit which is composed of four tempering heating furnaces, wherein the heat treatment furnaces are sequentially arranged from right to left as follows: a large high-temperature quenching heating furnace, a large tempering heating furnace, a small tempering heating furnace, a small tempering heating furnace, a small high-temperature quenching heating furnace, a small high-temperature quenching heating furnace and a small tempering heating furnace; and a set of matched high-precision cooling unit which is composed of cooling tanks with different specifications, wherein the cooling tanks are sequentially a clear water tank, an oil tank, a cleaning tank, an oil tank, a saline water tank, a clear water tank and an organic solvent tank from right to left.