To provide a heat transfer system and a method of operating the same, capable of distributing a refrigerant almost evenly to each evaporator without generating the gas deficiency in the operated evaporators.

In the heat transfer system which includes a condenser and two or more evaporators 9, forms a natural circulation cycle by connecting the condenser to the evaporator 9 through a refrigerant liquid pipe and a refrigerant gas pipe, and encloses the refrigerant in this natural circulation cycle, control valves 11 are provided on the upstream of two or more evaporators respectively and a control means 31 controlling each control valve at the time of startup is provided.